SUSPENDED: Analytical services
PROVIDED BY Instruct, Euro-BioImaging, VetBioNet, Emergen & Infravec
Get access to cutting-edge services & technologies for structural biology, imaging & sequencing
Browse our research resources and services
How to access our services FOR applications to all calls
All calls for proposals are now closed. You may contact the listed partners in the catalogue of services to get access to their facilities.
Three steps to get free-of-charge access to our services:
- Browse our catalogue and identify the service that you need
- Fill out the pre-application form at the bottom of the page and hit the ‘SUBMIT’ button
- After receiving an email with your ISIDORe ID number, follow the instructions to complete your application
Before you navigate our catalogue, please remember that:
- You will need an ORCID number. If you don’t already have one, please go to orcid.org to obtain your own in a few clicks.
- For multi-services requests, we’ll be happy to help: please contact us.
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Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Immunological assays (ELISA, Flow cytometry)
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Lung | |
| Nose | |
| Blood vessel | |
| Liver | |
| Kidney | |
| Brain | |
| 3D tissue and cell printer | |
| Animal | |
| Lung | Cattle |
| Intestinal | Cattle, Chicken |
Air Liquid Interface (ALI) polarised cells
| Human | |
| Lung | |
| Airway nasal | |
| Airway tracheal | |
| Airway bronchial | |
| CALU-3 | |
| A549 | |
| RPMI-2650 | |
| Animal | |
| Lung | Cattle, Chicken, Pig |
| Airway nasal | Sheep, Pig |
| Airway tracheal | Sheep, Pig, Mouse |
| Airway bronchial | Sheep, Pig |
| Intestinal | Cattle, Chicken |
Primary cells
| Human | |
| Immune cells ( macrophages, dendritic cells) | |
| Lung | |
| Cultures from surgical specimens | |
| Animal | |
| Immune cells (monocytes, macrophages, lymphocytes, dendritic cells) | Cattle, Sheep, Pig |
| Lung | Cattle, Sheep, Bat |
| Bronchial | Pig |
| Intestine | Bat |
Tissue section cultures
| Human | |
| Placental precision-cut slices | |
| Animal | |
| Lung Precision Cut slices | Mouse, Hamster, Pig, Sheep, Cattle, |
| Liver Precision Cut slices | Sheep |
Organotypic cultures
| Animal | |
| Lung | Chicken, Ferret, Pig |
| Trachea | Chicken, Ferret, Pig |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| HTR-8 | |
| RPMI-2650 | |
| HEPA-RG | |
| Nasal cell line | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
| Lung | Chicken |
| Bronchial | Pig |
Stem cells
| Human | |
| Mesenchymal | |
| Redifferentiated IPSCS (Induced pluripotent stem cells) | |
| Animal | |
| Mesenchymal | Cattle, Sheep, Pig, Mink, Rabbit |
Engineered cells
| Animal | |
| VERO HSLAM ((Human) signaling lymphocytic activation molecule) | African Green Monkey |
| VERO E6 with fluorescent viability reporter gene (m-Cherry-H2B (Histone-2B) Protein) | African Green Monkey |
Other
Custom cell requests may be considered.
| Human | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| Animal | |
| Preparation of tissues | Mammalian and Avian tissues |
| Preparation of little organs for clearing (Lungs) with I and U DISCO | Mouse |
Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Blood vessel | |
| Liver | |
| Kidney |
Air Liquid Interface (ALI) polarised cells
| Human | |
| A549 |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
Engineered cells
| Human | |
| HUH-7 expressing EBOV VP30 | |
| HUH-7 expressing MARV VP30 | |
| HUH-7 expressing SUDV VP30 | |
| A549 expressing EBOV VP30 | |
| A549 expressing MARV VP30 | |
| A549 expressing SUDV VP30 | |
| Animal | |
| VERO E6 expressing EBOV VP30 | African Green Monkey |
| VERO E6 expressing MARV VP30 | African Green Monkey |
| VERO E6 expressing SUDV VP30 | African Green Monkey |
Other
Custom cell requests may be considered.
| Human | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| Animal | |
| Preparation of tissues | Mammalian and Avian tissues |
All the services listed below are available for access regardless of the call for proposals and research topic that you select in your pre-application form.
SOCIAL SCIENCES SERVICES
Provided to you by: Sonar-Global
Contact
Sarah Marsh ARNAUD
sarah.arnaud@pasteur.fr
Social sciences preparedness and response interventions
- Vulnerability assessments
This service provides ethnographic investigation of locally-defined case definitions of social groups most likely to be marginalized or excluded before or during an epidemic; offer systematic analysis of complex factors leading to or aggravating marginalization - Protocols & implementation for public engagement, acceptability and compliance with epidemic control efforts: clinical trials, nonpharmaceutical interventions, and vaccination
This service will develop protocols for assessing the public engagement, acceptability and compliance with control efforts of targeted measures and if needed, support the implementation of these protocols
Post-intervention evaluation
- Intervention or response evaluation
Evaluation of the planning, development and implementation of specific epidemic intervention or response (including for COVID-19 pandemic) - Ethical evaluation: post-intervention assessment of ethical stakes at country level in West and Central Africa.
Service available for West and Central Africa French-speaking countries.
Evaluation of ethical dimensions/consequences of an intervention, (including and specific to the COVID-19 pandemic): Socio-anthropological assessment based on enquiries with national and local authorities, communities, teams and participants in the project. Offers assessment of social effects of program. Service is available for West and Central Africa French-speaking countries. - Ethical evaluation: Ethical assessment of program/intervention (elsewhere)
Evaluation of ethical dimensions/consequences of an intervention, (including and specific to the COVID-19 pandemic): Ethical evaluation of program or intervention by trained and experienced bioethics team
Scale-up services for qualitative analyses and epidemic response
- Demographic, health, socio-economic data and analyses
Scaling up of existing qualitative analyses to demographic, health and socio-economic data and analyses - Policy analysis
Systematic review of local policy measures and synthesis of key lessons learnt to inform scale-up in preparedness and ongoing response
Cost benefit analysis of epidemic response measure
- Cost benefit analysis of epidemic response measure
Evaluation of costs and benefits associated with public health intervention (including COVID-19), resulting in a report to be delivered at end of service
Community surveillance and social dimensions of outbreak investigation
- Design of community surveillance activities for human and animal health, to complement existing surveillance systems
Develop an adapted, locally appropriate plan for community detection of outbreaks of new COVID-19 waves. This service would enable local public health authorities to identify social risks and to facilitate community engagement and participation in the identification of these risks. Where appropriate, this plan will include human interactions with potential animal reservoirs in which COVID-19 has been detected. Rapid quantitative and qualitative methods, including key informant interviews and targeted focus group discussions will be employed - Design, implementation and supervision of community surveillance activities for human and animal health, to complement existing surveillance systems
Develop an adapted, locally appropriate plan for community detection of outbreaks of new COVID-19 waves. This service would enable local public health authorities to identify social risks and to facilitate community engagement and participation in the identification of these risks. Where appropriate, this plan will include human interactions with potential animal reservoirs in which COVID-19 has been detected. Rapid quantitative and qualitative methods, including key informant interviews and targeted focus group discussions will be employed - Development of protocol of social sciences community investigation of human/animal disease outbreak
This service will offer the development of a protocol to investigate the social dimensions of new outbreaks that may involve spill overs from animals into human beings (as well as spillbacks). The service will provide understanding of specific social, cultural and livelihood dimensions of human-animal interactions as well as concrete recommendations for prevention - Development and implementation of protocol of social sciences community investigation of human/animal disease outbreak
This service will offer the development and implementation of a protocol to investigate the social dimensions of new outbreaks that may involve spill overs from animals into human beings (as well as spillbacks). The service will provide understanding of specific social, cultural and livelihood dimensions of human-animal interactions as well as concrete recommendations for prevention
SERVICES FOR DISEASE VECTOR SURVEILLANCE
Provided to you by: Emergen & INFRAVEC
Contact
sequencing-services@isidore-project.eu
Sequencing services on disease surveillance can be found here.
- Vector field site access and training
- Spacial modelling
FieldWork
Provided to you by: INFRAVEC
Contact
TNAManager@infravec2.eu
Vector fieldwork Services
Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Immunological assays (ELISA, Flow cytometry)
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Lung | |
| Nose | |
| Blood vessel | |
| Liver | |
| Kidney | |
| Brain | |
| Animal | |
| Lung | Cattle, Sheep, Pig |
Air Liquid Interface (ALI) polarised cells
| Human | |
| Lung | |
| Airway nasal | |
| Airway tracheal | |
| Airway bronchial | |
| CALU-3 | |
| A549 | |
| Animal | |
| Lung | Cattle, Chicken |
| Airway nasal | Sheep |
| Airway tracheal | Sheep, Mouse |
| Airway bronchial | Sheep |
Primary cells
| Human | |
| Immune cells ( macrophages, dendritic cells) | |
| Cultures from surgical specimens (Rift valley fever virus model) | |
| Animal | |
| Immune cells (monocytes, macrophages, lymphocytes, dendritic cells) | Cattle, Sheep, Pig |
| Lung | Cattle, Bat |
| Bronchial | Pig |
| Intestine | Bat |
| Hepatocytes | Sheep |
| Maternal epithelial cells | Sheep |
| Umbilical cord derived endothelial cells | Sheep |
| Kidney | Chicken |
Tissue section cultures
| Human | |
| Lung precision-cut slices | |
| Placental precision-cut slices | |
| Animal | |
| Lung precision-cut slices | Mouse, Hamster, Pig, Sheep, Cattle, Chicken |
| Liver precision-cut slices | Sheep |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| HTR-8 | |
| BeWO | |
| HEPA-RG (Rift Valley fever virus model) | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
| Lung | Chicken |
| UMNSAH/DF-1 | Chicken |
| Bronchial | Pig |
| Neuro-2a | Mouse |
| C6/36 | Aedes albopictus |
| Aag2 | Aedes aegypti |
Stem cells
| Human | |
| Mesenchymal | |
| Animal | |
| Mesenchymal | Sheep |
Other
Custom cell requests may be considered.
| Human | |
| Neuronal/Glial cells | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| 3D-vessel-on-a-chip | |
| Animal | |
| Transplacental model (maternal epithelial cells and trophoblasts) | Sheep |
| 3D-vessel-on-a-chip | |
| Preparation of tissues | Mammalian and Avian tissues |
Structural Biology Services
Provided to you by instruct
Contact
Pauline AUDERGON
isidore@instruct-eric.org
The services listed below are available for access regardless of the call for proposals and research topic you select in your pre-application form.
Nanobody discovery
- Generation and characterisation of conformational nanobodies (to facilitate the structural analysis of proteins that are notoriously difficult to purify, to crystallize or to study by another method.)
- Rapid selection of nanobodies by screening/affinity maturation
Crystallography
- Crystallisation of Proteins and Nucleic Acids
- High-throughput Crystallisation
- CrystalDirect Online Crystallography protein-to-structure pipeline
- IceBear crystallography data management (data management, crystallization, data collection)
ISIDORe Services in action:
Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. doi.org/10.1038/s41467-020-17495-9
Protein production for Structural Biology
- Protein expression
- Cloning
- High throughput expression
- Protein purification
- Biomolecular complex purification
Molecular Biophysics
Wide range of techniques to study the biophysical characterization of the structure, function and stability of biological macromolecules like proteins, nucleic acids, lipids and their complexes; as well as the kinetic and thermodynamic parameters of their interaction.
- Circular Dichroism
- Differential Scanning Fluorescence
- Differential Scanning Calorimetry
- Dynamic Light Scattering
- UV/Vis Spectrometry
- Microscale Thermophoresis
- Surface Plasmon Resonance,
- High Throughput Biolayer Interferometry
- Isothermal titration Calorimetry
- Antibody screening in patient sera (Robotein automated Bimolecular analysis platform)
- SEC-MALS (multi-angle light scattering)
ISIDORe Services in action:
Poor antibody response to BioNTech/Pfizer COVID-19 vaccination in SARS-CoV-2 naïve residents of nursing homes. doi:10.1093/cid/ciab998
Single Molecule and Super-Resolution Microscopy for Structural Biology applications (Instruct)
- Single-molecule detection with fluorescence microscopy techniques: using widefield microscopy such as TIRF, super-resolution methods SMLM (STORM, GSD/GSDIM, PALM, PAINT)
Mass Spectrometry
- Native mass spectrometry
- Single cell mass spectrometry
- Proteomic mass spectrometry with possibility for plasma proteome analysis including monitoring of viral and immune response proteins, analysis of single viral proteins and binding to drugs and antibodies
- Glycan analysis by Mass spectrometry
- GC-MS for the analysis of cuticle thickness to test insecticide resistance in mosquitoes
ISIDORe Services in action:
ICAM-1 induced re-arrangements of capsid and genome prime rhinovirus 14 for activation and uncoating. doi.org/10.1073/pnas.2024251118
Electron Microscopy techniques for Structural Biology
- Scanning electron microscopy (SEM)
- Transmission electron microscopy (TEM)
- Cryogenic electron microscopy (Cryo-EM)
- Electron Microscopy Data Processing Services
- Electron tomography
- Cryo-Electron tomography
- Cryo-Correlative Light and EM
ISIDORe Services in action:
Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects macaques from infection. doi: 10.1016/j.xcrm.2022.100528
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. doi: 10.1126/science.abd5223
Magnetic Resonance Techniques
- Solution NMR
- Solid state NMR
- Fragment-screening by NMR
- NMR metabolomic
- NMR-based screening of protein-drug interactions
- Glycan analysis by NMR
ISIDORe Services in action:
The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a. doi: 10.1126/sciadv.abm4034
In-Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells. doi:10.1002/anie.202007184
X Ray Structural Biology Techniques
- X-ray crystallography
- Biological small angle scattering (Bio-SAXS),
- X-ray imaging from synchrotron sources
- XChem Fragment Screening
ISIDORe Services in action:
The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a. doi: 10.1126/sciadv.abm4034.
PDB-REDO
Procedure to optimise crystallographic structure models, providing algorithms that make a fully automated decision-making system for refinement, rebuilding and validation.
- PDB-REDO
AlphaFill
AlphaFold models enriched with ligands and co-factors.
- Alphafill
IMAGING SERVICES
Provided to you by Euro-BioImaging ERIC & VetBioNet
Contact
Arina RYBINA info@eurobioimaging.eu
How imaging technologies contribute to understanding viruses
Imaging technologies used to understand COVID-19 infection
Imaging techniques and COVID19 diagnosis
Understanding SARS-CoV-2 replication cycle in human cells
All the services listed below are available for access at BSL-1 or BSL-2 regardless of the call for proposals & research topic that you select in your pre-application form.
Preparation of samples at BSL3 might be accommodated as part of the service.
Imaging services that can be provided directly in BSL-3 containment are marked with an *
Light Microscopy & Advanced Light Microscopy for Biological Imaging
Fluorescence microscopy
- Laser scanning confocal microscopy (LSCM/CLSM)
- Spinning disc confocal microscopy (SDCM)*
- Light sheet microscopy (LSM) and lattice light sheet microscopy (LLSM)
- Structured illumination microscopy (SIM)
- Widefield microscopy: Total internal reflection fluorescence microscopy (TIRF)
- Deconvolution widefield microscopy (DWM)*
- Image scanning microscopy
- Two-Photon Microscopy/Multi-photon microscopy systems
Fluorescence Nanoscopy
- Stimulated Emission Depletion Microscopy (STED)
- Single-molecule localisation microscopy techniques (SMLM): STORM, GSD/GSDIM, PALM
- Reversible optical fluorescence transitions (RESOLFT)
- Super-resolution localization microscopy – localization super-resolution experiments (SMLM: dSTORM, GSDIM, STORM, PALM, PAINT), particle tracking, standard wide-field epifluorescence and TIRF microscopy, transmission microscopy.
- MINFLUX
Functional Imaging and Specialized Technologies
- High-throughput microscopy (HTM)/High content screening (HCS), RNAi screens
- Protein dynamics and interactions (FRET, FCS, FCCS, FLIM, FRAP)
- Multi-photon microscopy
- High resolution episcopic microscopy (HREM)
- Photomanipulation
- High speed imaging
- Feedback microscopy
- Cryo-FM
Mesoscopic Imaging
- Light Sheet mesoscopic imaging: Single-plane illumination microscopy (SPIM), dSLSM
- Optical projection tomography (OPT)
Label-free Imaging
- Quantitative phase imaging (QPI)
- Raman spectroscopy
- Coherent Anti-Stokes Raman Scattering microscopy (CARS)
ISIDORe Services in action
3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations. doi:10.1093/bioinformatics/bty200. Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera
doi: 10.1002/bies.202000257
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003
Virus morphology: Insights from super-resolution fluorescence microscopy
doi: 10.1016/j.csbj.2021.10.038
Sample Characterization
- Atomic force microscopy (AFM)
- MSI - Mass Spectrometry - based Imaging
Electron microscopy for Biological Imaging / Ultrastructural Analysis in 2D & 3D
- Scanning electron microscopy (SEM), including 3D SEM of plastic embedded samples
- Array tomography
- Focused-ion-beam scanning EM (FIB-SEM)
- Serial Block Face Scanning EM (SBF-SEM or SBEM)
- Transmission Electron Microscopy, including Serial section TEM (ssTEM)
- TEM tomography, STEM tomography
- Cryogenic electron Microscopy (Cryo-EM: Cryo-ET, Cryo-SEM, Cryo-FIB, Cryo-TEM)
- Immuno-electron microscopy (immunogold labelling of Tokuyasu cryosections)
ISIDORe Services in action
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003
SARS-CoV-2 infection induces the dedifferentiation of multiciliated cells and impairs mucociliary clearance doi.org/10.1038/s41467-021-24521-x
Correlative Light Microscopy & Electron Microscopy for Biological Imaging
- CLEM from live cells to plastic sections ("live" CLEM)
- Correlative light-electron microscopy from live cells to 3D plastic embedded samples
- Intravital CLEM
- High accuracy on section CLEM
- CLEM on Tokuyasu sections
- CryoCLEM
ISIDORe Services in action
Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies doi.org/10.1038/s42003-020-01567-z
Phase contrast X-Ray Imaging
- Phase contrast X ray imaging (PCI)
ISIDORe Services in action
3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography doi: 10.7554/eLife.60408
Animal imaging (multimodal imaging of small animals)
- Multimodal imaging of small animals
- In vivo optical imaging
- Intravital microscopy
- Magnetic Resonance Imaging (MRI)
- Ultra-sound imaging (US)
- Computed tomography (CT)
- Nuclear imaging (PET, SPECT)
- Bimodal technologies
- Provision of imaging probes/tracers
Animal Monitoring
- Animal behaviour monitoring
- Quantitative spatial-temporal monitoring of individual animals and groups using TrackLab or EthoVision XT software (computer vision, UWB, GPS sensors)
- Computer-aided monitoring: Registration and analysis of manual observations of animals directly or with video feeds/films, potentially including synchronization of data streams, e.g., of physiology by means of The Observer XT
- Animal physiology monitoring
- Body temperature (combined with other variables as required), physiology sensors dependent on the animal species and variables required
Histopathology
- Histopathology
Image Data & Image Analysis
- Biological and Bio-Medical Image data analysis, including consultation and development of novel analysis and visualisation solutions
- AI and Machine Learning (ML)
- Medical Image Data Archiving
ISIDORe Services in action
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003
Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera doi: 10.1002/bies.202000257
Sequencing SERVICES
Provided to you by Emergen & INFRAVEC
Contacts
sequencing-services@isidore-project.eu
The services listed below are available for access regardless of the call for proposals and research topic you select in your pre-application form.
** These services can be provided in combination with or without bioinformatics support.
Genomic sequencing services (BACTERial / viral DNA / RNA genome)
- Illumina technology**
- Oxford Nanopore technology
- Bacterial Genome Sequencing
ISIDORe Services in action
Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075
Metagenome sequencing services
- Shotgun metagenome sequencing (AP-HP CHU Henri Mondor Technologie patent and accreditation): identification of any microorganism (up to 100/week)
- Viral metagenome sequencing: identification of any virus (up to 100/week)
- 16S rRNA metagenome sequencing
- Pan-pathogen surveillance through shotgun metagenomics
ISIDORe Services in action
Identification of necrotizing dermohypodermitis and fasciitis causative microbial agents and microbiota by targeted and shotgun metagenomics
doi: 10.1111/bjd.18611
Inclusion-Body Encephalitis Detected and Characterized by Standardized and Validated Shotgun Metagenomic Approach
doi: 10.3201/eid2609.200366
Fatal Encephalitis Caused by Cristoli virus, a New Emerging Member of the Orthobunyavirus genus of the Peribunyaviridae family
doi: 10.3201/eid2606.191431
Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms
doi: 10.3390/microorganisms8101539
Metagenomic Investigation of Torque Teno Mini Virus-SH in Hematological Patients
doi: 10.3389/fmicb.2019.01898
Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management
doi:10.3390/v10110633
Quality Control Implementation for Universal Characterization of DNA and RNA Viruses in Clinical Respiratory Samples Using Single Metagenomic Next-Generation Sequencing Workflow
doi:10.1186/s12879-018-3446-5
Metatranscriptome sequencing services
- Viral metatranscriptomic – Whole genome sequencing of RNA viruses, including SARS-CoV-2 (up to 100 /week)
ISIDORe Services in action
Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075
Miscellaneous sequencing services
- Small RNA Illumina sequencing**
- Long read DNA sequencing by Nanopore**
- RNAseq total transcriptome Illumina sequencing**
- Genotyping of mosquitoes, insecticide resistance and detection of pathogens
ISIDORe Services in action
Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075
Respiratory pathogens (non-SARS-CoV-2)
Coronaviridae, Orthomyxoviridae, etc.
Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Immunological assays (ELISA, Flow cytometry)
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Lung | |
| Nose | |
| Blood vessel | |
| Liver | |
| Kidney | |
| Brain | |
| 3D tissue and cell printer | |
| Animal | |
| Lung | Pig |
Air Liquid Interface (ALI) polarised cells
| Human | |
| Lung | |
| Airway nasal | |
| Airway tracheal | |
| Airway bronchial | |
| CALU-3 | |
| A549 | |
| Animal | |
| Airway nasal | Sheep |
| Airway tracheal | Sheep, Mouse |
| Airway bronchial | Sheep |
Primary cells
| Human | |
| Immune cells (macrophages, dendritic cells) | |
| Animal | |
| Immune cells (monocytes, macrophages, lymphocytes, dendritic cells) | Cattle, Sheep, Pig |
| Bronchial | Pig |
| Lung | Bat |
| Intestine | Bat |
| Kidney (Avian infectious bronchitis virus model) | Chicken |
| Embryo Kidney (Avian Influenza model) | Chicken |
Tissue section cultures
| Human | |
| Lung precision-cut slices | |
| Placental precision-cut slices | |
| Animal | |
| Lung precision-cut slices | Mouse, Hamster, Pig, Sheep, Cattle, Chicken |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| HTR-8 | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
| DF1 Embryonal fibroblasts | Chicken |
Stem cells
| Human | |
| Mesenchymal | |
| Animal | |
| Mesenchymal | Cattle, Sheep, Pig, Mink, Rabbit |
Engineered cells
| Animal | |
| VERO HSLAM ((Human) signaling lymphocytic activation molecule) | African Green Monkey |
Other
Custom cell requests may be considered.
| Human | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| Animal | |
| Embryonated Specific Pathogen Free Eggs (Avian Influenza model) | Chicken |
| Preparation of tissues | Mammalian and Avian tissues |
Cell model - immortalised cell lines
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Vero E6
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability (incl. high content imaging)
- Bioimaging/Microscopy (incl. high content imaging)
- Flow cytometry
- Immunohistochemistry
- Histological methods
Vero CCL81
- Virus isolation
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR (E, RdRP, N, S)
- Omics - spatial transcriptomics
- Sequencing - NGS
- ELISA (N)
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
- Flow cytometry
- Luminex assay for antibody detection
- Histopathology
- Immunohistochemistry
- Histological methods
Calu 3
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
- Flow cytometry
- Immunohistochemistry
- Histological methods
A549
- Virus titration
- Neutralization assay
- Cytotoxicity
- Antiviral assay
- CPE (TCID50)
- qRT-PCR
- Immunofluorescence
- Cell viability (incl. high content imaging)
- Bioimaging/Microscopy ((conventional - high resolution confocal microscopy ; high content imaging)
Caco-2
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
MDCK
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Hep-2
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Huh-7
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
RPMI-2650
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
human nasal cell line
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Chicken lung epithelial cells
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR - primer sets for chicken innate immune genes)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Pig bronchial epithelial cells
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Cell model - primary cells
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
pig macrophages
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
pig monocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
pig lymphocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
sheep monocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
sheep macrophages (monocyte-derived)
- Virus titration
- Neutralization assay
- Antiviral assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
sheep macrophages (alveolar)
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
sheep macrosheep lymphocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
human primary epithelial lung cells (monolayers/polarised 2D culture)
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
bovine primary epithelial lung cells (monolayers/polarised 2D culture)
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
ovine primary epithelial lung cells (monolayers/polarised 2D culture)
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
cattle macrophages (monocyte-derived)
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
cattle macrophages (alveolar)
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
primary human cell cultures from surgical specimens
- Virus isolation
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Bat lung epithelial cells
- Virus isolation
- Virus titration
- Antiviral assay
- CPE (TCID50)
- qRT-PCR (E, RdRP, N, S)
- Sequencing - NGS
- ELISA (N)
- Immunofluorescence
- Luminex assay for antibody detection
- Histopathology
Bat intestine epithelial cells
- Virus isolation
- Virus titration
- Antiviral assay
- CPE (TCID50)
- qRT-PCR (E, RdRP, N, S)
- Sequencing - NGS
- ELISA (N)
- Immunofluorescence
- Luminex assay for antibody detection
- Histopathology
Swine bronchial epithelial cells
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR )
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Cell model - mesenchymal stem cells
Provided to you by VetBioNet, ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
rabbit mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
mink mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
bovine mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
pig mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
Cell model - Well differentiated and/or polarised cell systems
Provided to you by VetBioNet, ERINHA & EMBRC
Contact
exvivo-invivo-services@isidore-project.eu
ALI-differentiated 2D culture of primary human lung cells
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
ALI-differentiated 2D culture of primary bovine lung cells
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Calu-3 differentiated in ALI conditions
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
A549 differentiated in ALI conditions
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Chicken lung epithelial cells - ALI
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR - primer sets for chicken innate immune genes)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Pig bronchial epithelial cells - ALI
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
RPMI-2650 in ALI 2D cultures
- Vi
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Non-conventional screening models for toxicity and ecotoxicity
Non-conventional screening models for toxicity and ecotoxicity assays:
- zebrafish eggs: up to 48h, 96 well format
- invertebrates (rotifers and artemia): 96 well format
- microalgae
Cell model - Engineered cell lines and primary cells
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Vero hSLAM ((human) signaling lymphocytic activation molecule)
- Virus isolation
- Virus titration
- Neutralization assay
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
- Histopathology
- Immunohistochemistry
- In situ hybridization
Vero E6 with fluorescent viability reporter gene (m-cherry-H2B (histon-2B) protein)
- Cytotoxicity (combined with high-content imaging)
- Cell viability (high-content imaging)
- Bioimaging/Microscopy (high-content imaging)
redifferentiated iPSCs (induced Pluripotent Stem Cells)
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Cell model - Other 2D cell model
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Preparation of mammalian tissues
- Cloning (Cell sorting on plates - 96, 384…)
- Immunofluorescence (conventional and confocal microscopy)
- Bioimaging / microscopy (conventional and confocal microscopy)
- Flow cytometry (multicolor flow cytometry, High Speed cell sorting)
- Histopathology (histology / immunochemistry)
Preparation of avian tissues
- Cloning (Cell sorting on plates - 96, 384…)
- Immunofluorescence (conventional and confocal microscopy)
- Bioimaging / microscopy (conventional and confocal microscopy)
- Flow cytometry (multicolor flow cytometry, High Speed cell sorting)
- Histopathology (histology / immunochemistry)
Swab / saliva collection devices
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Cell model - Organoids
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
human lung organoids
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
bovine lung organoids
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
3D tissue and cell printer
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Cell model - Precision-cut tissue slices cultures
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Bovine lung PCLS (Precision Cut Lung Slices)
- qRT-PCR (Fluidigm medium-throughput qPCR - primer sets for >200 bovine genes, mainly related to immunity)
- ELISA (IL-8; IL-1b,…..)
- Immunofluorescence (confocal microscopy)
- Cell viability (LDH release assay)
Hamster PC lung tissue
- Virus isolation
- Virus titration
- Neutralization assay
- Typing
- Omics - transcriptomic analysis by nanostring assay
- Sequencing - NGS
- Histopathology (incl. Immunohistology)
Sheep primary lung PCLS
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
Cattle primary lung PCLS
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
Mouse primary lung PCLS
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
Cell model - Organotypic culture
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Chicken tracheal culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Chicken lung culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Ferret tracheal culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Ferret lung culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Pig tracheal culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Pig lung culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Cell model - Other 3D cell models
Preparation of little organs for clearing (lung of mouse) with i and u DISCO
- Cloning (Cell sorting on plates - 96, 384…)
- Immunofluorescence (conventional and confocal microscopy)
- Bioimaging / microscopy (conventional and confocal microscopy)
- Flow cytometry (multicolor flow cytometry, High Speed cell sorting)
- Histopathology (histology / immunochemistry)
SERVICES PROVIDED TO YOU BY: VetBioNet, Transvac, Infrafrontier, ERINHA & EMBRC
ISIDORe will only offer access to in vivo models in the absence of adequate alternative methods to achieve an identical result (REPLACE). Please do not forget to check out our wide range of EX VIVO MODELS.
When in vivo models cannot be substituted with any other comparable method, we will use the smallest number necessary for quality science (REDUCE), as well as state-of-the-art practices to protect animal welfare and prevent animal pain and distress (REFINE).
Positively evaluated requests for access to in vivo models will be subjected to institutional ethical evaluation before any implementation can happen.
The services listed below are a general overview of ISIDORe’s in vivo capacities. Models are not available for all species and/or all pathogens. If you want to make sure that we can provide access to your model of interest, please contact us: exvivo-invivo-services@isidore-project.eu
MODELS FOR INFECTION STUDIES
Please note that agents from the Plasmodiidae and Trypanosomatidae famililes can only be studied in Arthropods. Main exceptions are indicated in brackets. Other specific exceptions may apply.
Provided to you by: VetBioNet, Infrafrontier & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse1
- Hamster (available for RG4 pathogens)
- Guinea Pig (not available for vector-borne pathogens)
- Rabbit
- Ferret
- Pig1,3
- Sheep5 (not available for RG4 pathogens)
- Cattle (not available for RG4 pathogens)
- Non-human primates
- Livestock
- Camelids (not available for RG4 pathogens)
- Chicken2 (not available for RG4 pathogens)
- Fruitbats (not available for RG4 pathogens)
- Wildlife2,4 (not available for RG4 pathogens)
- Zebrafish (not available for RG4 pathogens)
- Arthropods (Only available for vector-borne pathogens)
1 Includes models expressing human ACE2
2 Includes avian influenza models
3 Includes pig influenza models
4 Includes vector-transmission models
5 Includes pregnant sheep models
MODELS FOR DRUG EFFICACY STUDIES
Please note that agents from the Plasmodiidae and Trypanosomatidae famililes can only be studied in Arthropods. Main exceptions are indicated in brackets. Other specific exceptions may apply.
Provided to you by: VetBioNet, Infrafrontier & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse1
- Hamster (not available for RG4 pathogens)
- Guinea Pig (not available for vector-borne pathogens)
- Rabbit
- Ferret
- Pig1,3
- Sheep5 (not available for RG4 pathogens)
- Cattle (not available for RG4 pathogens)
- Non-human primates
- Livestock
- Camelids (not available for RG4 pathogens)
- Chicken2 (not available for RG4 pathogens)
- Fruitbats (not available for RG4 pathogens)
- Wildlife2,4 (not available for RG4 pathogens)
- Zebrafish (not available for RG4 pathogens)
- Arthropods (Only available for vector-borne pathogens)
1 Includes models expressing human ACE2
2 Includes avian influenza models
3 Includes pig influenza models
4 Includes vector-transmission models
5 Includes pregnant sheep models
MODELS FOR VACCINE EFFICACY STUDIES
Please note that agents from the Plasmodiidae and Trypanosomatidae famililes can only be studied in Arthropods. Main exceptions are indicated in brackets. Other specific exceptions may apply.
Provided to you by: VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse1
- Hamster (not available for RG4 pathogens)
- Guinea Pig (not available for vector-borne pathogens)
- Rabbit
- Ferret
- Pig1,3
- Sheep5 (not available for RG4 pathogens)
- Cattle (not available for RG4 pathogens)
- Non-human primates
- Livestock
- Camelids (not available for RG4 pathogens)
- Chicken2 (not available for RG4 pathogens)
- Fruitbats (not available for RG4 pathogens)
- Wildlife2,4 (not available for RG4 pathogens)
- Zebrafish (not available for RG4 pathogens)
- Arthropods (Only available for vector-borne pathogens)
1 Includes models expressing human ACE2
2 Includes avian influenza models
3 Includes pig influenza models
4 Includes vector-transmission models
5 Includes pregnant sheep models
MODELS FOR VACCINE IMMUNOGENICITY STUDIES
Provided to you by: VetBioNet, Transvac & EMBRC
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse
- Hamster
- Rabbit
- Ferret
- Pig
- Sheep
- Cattle
- Non-human primates
- Camelids
- Chicken
- Wildlife Zebrafish
MODELS FOR VECTOR RESEARCH
All of the vectors listed below can be provided free of pathogens. Some of the vectors listed below are provided ONLY free of pathogens and are marked with an *. If you want to make sure that we can provide access to your vector of interest, please contact us.
Provided to you by: INFRAVEC
Contact
TNAManager@infravec2.eu
| Aedes spp | (available pathogen-free and carrying members of the Flaviviridae, Togaviridae & Trypanosomatidae1 families) |
| Anopheles spp | (available pathogen-free and carrying members of the Flaviviridae and Plasmodiidae families) |
| Culex spp | (available pathogen-free and carrying members of the Flaviridae family) |
| Culocoides spp* | (avalaible pathogen-free only) |
| Glossina spp* | (avalaible pathogen-free only) |
| Hyalomma spp* | (avalaible pathogen-free only) |
| Lutzomyia spp | (available pathogen-free and carrying members of the Trypanosomatidae1 family) |
| Ornithodoros spp* | (avalaible pathogen-free only) |
| Phlebotomus spp | (available pathogen-free and carrying members of the Trypanosomatidae1 family) |
| Rhipicephalus spp* | (avalaible pathogen-free only) |
| Sergentomyia spp | (available pathogen-free and carrying members of the Trypanosomatidae1 family) |
| Stomoxys spp* | (avalaible pathogen-free only) |
Mosquito mass rearing* (up to 1000, 10 000, 100 000 specimens) may be available under request.
1 including Leishmania
GENERATION OF NEW STUDY MODELS FOR SARS-CoV-2 RESEARCH
Provided to you by: Infrafrontier
Contact
Asrar Ali KHAN
asrar.khan@infrafrontier.eu
- Generation of precision mouse models
- Humanization of mouse model cohorts by AAV-driven hACE2 expression
- Generation of knock-out mice (service starting 2023)
- Generation of knock-in mice (service starting 2023)
DETECTION & CHARACTERIZATION OF IMMUNE TISSUES & CELLS
Provided to you by: EATRIS, VetBioNet, Infrafrontier & ERINHA
Contact
Patricia Carvajal-Vallejos
patriciacarvajal@eatris.eu
- Immune-function profiling
This service is available for access regardless of the call for proposals and research topic that you select in your pre-application form. Antigen-specific T proliferation and cytokine, chemokine and immune factor analysis (mass cytometry, FACSCanto, LSR IV, Symphony, Helios, Bio-Plex Multiplex immunoassay). - Immune-cell profiling
This service is available for access in the following calls for proposals: CALL I (SARS-CoV-2), CALL IV (non-SARS-CoV-2 respiratory pathogens), CALL V (vector-borne pathogens), and CALL VI (Other epidemic-prone pathogens). - Antiviral screening & mucosal immunology
This service is available for access for SARS-CoV-2 research projects. Including human airway models for testing drugs and for virus – cells interaction, to evaluate the role of individual immune subsets in different contexts against infectious disease and to characterize viral isolates. - Detection and quantification of SARS-CoV-2-specific T cells at the single cell level
This service is available for access for SARS-CoV-2 and MPXV research projects - T-cell cloning and expansion
This service is available for access for SARS-CoV-2 research projects. Determination of specificity - Detection and quantification of SARS-CoV-2-specific B cells at the single cell level
This service is available for access for SARS-CoV-2 research projects. - Access to organoids, spheroids & multifluidic devices for immune surveillance (IncuCyte live-cell imaging of spheroids)
This service is available for access for SARS-CoV-2 research projects.- Virus sequencing, non-coding RNA expression and antibody responses to viral antigens with high-content imaging and analysis.
- Access to Multi-site Immuno-analysis of SARS-CoV-2, including analysis of infected samples based on metal tag detection by mass cytometry
DETECTION & CHARACTERIZATION OF THE IMMUNE RESPONSE
Provided to you by: EATRIS, VetBioNet & ERINHA
Contact
Patricia Carvajal-Vallejos
patriciacarvajal@eatris.eu
- Medium‑ to large-scale analysis of immune proteins
The services listed below are available for access for SARS-CoV-2 research projects.- Protein/peptide identification
- Antibody Characterization / Multi-Attribute Method (MAM)
- Post-Translational Modifications Analysis (Glycosylation; Oxidation/Deamination, Glycan Identity)
- High-throughput Quantitative Proteomics – SWATH analysis (untargeted; relative quantification)
- Intact Protein Measurement
- Aggregation and refolding (SEC chromatography)
- Antibody profiling to evaluate the host immune response
- ICS-T-cell-responses (TRM), Virus-immunome profiling
Quantification of cytokines/chemokines (Bio-plex Multiplex Immunoassay), surface and intracellular detection of markers/cytokines (flow cytometry) in infected biological samples - Functional studies of pathogenicity of genetic variants at molecular and cellular level
Including virus sequencing, non-coding RNAs expression and ELISA assay, drugs; drug testing - Epigenetics of immune cells
To study genome-wide epigenetic changes including DNA methylation, histone modifications and non-coding RNAs expression - Immunoprofiling in swine and poultry
Polychromatic flow cytometry assays, single cell immunomics, MHC haplotyping, Luminex cytokine profiling
DETECTION, CHARACTERIZATION & MODULATION OF IMMUNE GENE EXPRESSION
Provided to you by: EATRIS & VetBioNet
Contact
exvivo-invivo-services@isidore-project.eu
The services listed below are available for access regardless of the call for proposals and research topic that you select in your pre-application form.
- siRNA libraries
- Human
- Swine
- Poultry
- sgRNA/CRISPR Cas9 knockout libraries
- Human
- Swine
- Poultry
- Cattle
- RNAseq transcriptomics, 16S NGS microbiome analysis, metabolomics (LC-MS) in livestock
- Swine
- Poultry
- Specific primer sets and protocols for medium-throughput Fluidigm qPCR targeting up to 96 immune genes
- Mice
- Swine
- Cattle
- Chicken
BIO IMAGING FOR IMMUNO PROFILING
Provided to you by: Euro-BioImaging
Contact
info@eurobioimaging.eu
All the services listed below are available for access at BSL-1 or BSL-2 regardless of the call for proposals & topic you select.
- Development and validation of imaging probes
Targeting of specific molecular inflammation markers or subpopulations of immune cells in surrogate infection models in vivo - Biomedical imaging technologies for monitoring the immune system
- PET
- MRI
- CT
- US
- Optical imaging
- Multimodal imaging
- High-throughput Imaging & Bioimage Analysis
PerkinElmer Opera Phenix & Molecular Devices ImageXpress Nano. Automation for sample processing and Imaging in both +37 C and RT. Image analysis pipelines and customized solutions for DNN based segmentation & classification in 2D and 3D.
SUPPORT FOR THE DEVELOPMENT OF DIAGNOSTICS
Provided to you by the Biomedical Research Foundation, Academy of Athens (BRFAA), the Joanneum Research (JR), and Joint Research Center of European Commission (JRC) in collaboration with EU-OPENSCREEN
Due to the high demand in EU-OPENSCREEN services to support Diagnostic and Therapeutic Development, there is insufficient EC funding to provide you with our services at this time. Feel free to submit a pre-application to enter your research proposal into our list of potential future projects. They will be considered in received order, should additional funding become available in the future. Thank you very much for your understanding.
Contact
EU-OPENSCREEN scientific-projects
scientific-projects@eu-openscreen.eu
Charlotte Wit
charlotte.wit@eu-openscreen.eu
All the services listed below are available for access at BSL-1 or BSL-2 regardless of the call for proposals & research topic that you select in your pre-application form:
- Characterization of in-vitro diagnostic devices and sensing platforms
Electron microscopy (SEM-EDX, TEM-EDX); Surface analysis (XPS, TOF-SIMS); Raman Microscope; Array scanner - Assay development (molecular and biochemical) and integration to IVD devices
Customization of existing assays to be integrated into LoCs, biosensors and microfluidics-based devices - Testing of developed and optimized assays, biosensors, LoCs and microfluidics-based devices with well-characterized samples
Extensive biobank of blood & nasopharyngeal samples from patients infected with various viral and bacterial pathogens. - Surface functionalization
Development of surface modification techniques towards biomolecule immobilization and biosensor fabrication or tailoring of surface properties (antifouling, surface energy etc.) - Lab-on-a-Chip molecular diagnostics, multiplexed pathogen detection, variant discrimination
- Lab-on-a-chip design
Simulation-based fluidics design for existing assays - Lab-on-a-chip implementation
Implementation and adaptation of existing assays into foil-based lab-on-chip - Lab-on-a-chip demonstrator
Foil-based lab-on-chip demonstrator device development for existing assays - Matrix customized methods (e.g., non-human samples) and multiplexed pathogen detection
Development/application of rapid, low cost, high throughput molecular methods for population screening
VECTOR MONITORING
Provided to you by INFRAVEC
Contact
TNA Manager
TNAManager@infravec2.eu
Personalized training in the development and application of molecular diagnostics for vector monitoring
Personalized (1-2 people) laboratory training in state-of-the art molecular biology laboratories to develop and apply molecular diagnostics relevant for modern vector monitoring.
Once you have submitted the ISIDORe pre-application below, please complete the Full application for access to this Personalized Training.
Access to the personnal training application
SUPPORT FOR THE DEVELOPMENT OF SMALL MOLECULE THERAPEUTICS
Provided to you by: EU-OPENSCREEN, EU-OPENSCREEN Partners, ERINHA & EMBRC
Due to the high demand in EU-OPENSCREEN services to support Diagnostic and Therapeutic Development, there is insufficient EC funding to provide you with our services at this time. Feel free to submit a pre-application to enter your research proposal into our list of potential future projects. They will be considered in received order, should additional funding become available in the future. Thank you very much for your understanding.
Contacts
EU-OPENSCREEN scientific-projects
scientific-projects@eu-openscreen.eu
Charlotte Wit
charlotte.wit@eu-openscreen.eu
All the services listed below are available for access regardless of the call for proposals & research topic that you select in your pre-application form. The maximum biosafety level of containment for the performance of the experiments is indicated in the description of the services. For confirming the feasibility of your request, please contact us.
Small molecule libraries – provided ONLY in combination with high throughput screening (HTS) services offered below
- Repurposing Library
Preparation of assay-ready plates with drug repurposing libraries containing approved and clinical trial compounds - European Chemical Biology Library (ECBL)
Preparation of assay-ready plates with 100.000 small molecules containing approx. 2464 bioactives - EU-OPENSCREEN Fragment Library
Preparation of plates with approx. 1000 fragments including 88 minifrags - EU-OPENSCREEN Bioactives
Preparation of plates with 2464 bioactives
Assay development, high throughput screening and hit profiling services for identification of active small molecule and host-targeting agents
- Assay development
Assay design and development in a broad range of readouts including phenotypic assays in BSL2-BSL3 facilities (bacterial growth inhibition and viral infection inhibition, cell-based HCS, host cell response), and BSL1 in-vitro target-based assays with specific bacterial, viral and human targets - Biochemical and enzymatic target-based high-throughput screening
High-throughput screening using BSL1 in-vitro target-based assays with specific bacterial, viral and human targets. The assay needs to be HTS-compatible with demonstrated performance in 384-well format. The service includes assay transfer, HTS and hit validation
Do not forget to request library if necessary. - Cell-based high-throughput screening
Cell-based screen including phenotypic, and target-based that can be run in both, human and bacterial, cells in BSL2 facilities. The assay needs to be HTS-compatible with demonstrated performance in 384-well format. The service includes assay transfer, HTS and hit validation
Do not forget to request library if necessary - Low- and medium-throughput screening in BSL3 facilities
Cell-based screen including phenotypic, and target-based that can be run in human cells and pathogen infection models in BSL3 facilities. The service includes assay transfer, screening and hit validation - Fragment screening
Includes assay development, screening and hit validation - Hit validation and profiling
Disease-relevant models, ADMET, ROS‑tox and others
ISIDORe Services in action
The blood-brain barrier is dysregulated in COVId-19 and serves as a CNS entry route for SARS-CoV-2 doi.org/10.1016/j.stemcr.2021.12.011
Characterization of ACE Inhibitors and AT1R Antagonists with Regard to Their Effect on ACE2 Expression and Infection with SARS-CoV-2 Using a Caco-2 Cell Model
doi.org/10.3390/life11080810
X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease
doi: 10.1126/science.abf7945
Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen
doi.org/10.1021/acsptsci.0c00216
A SARS-CoV-2 cytopathicity dataset generated by high-content screening of a large drug repurposing collection
doi.org/10.1038/s41597-021-00848-4
EVALUATION OF THE SELECTIVE ANTIVIRAL ACTIVITY OF AGENTS IN VIRUS-CELL-BASED ASSAYS
Medicinal chemistry support
- Drug design & evaluation in silico
- Hit-to-lead development following HTS of small molecules
- Fragment-to-lead development fragment screening
- Optimization of potency, selectivity and in vitro/in vivo ADMET properties of small molecule drug candidates
- Design and synthesis of target degraders (PROTACs, RIBOTACs)
Natural compound libraries
provided by EMBRC
Contact
Davide Di Cioccio
davide.dicioccio@embrc.eu
- Natural compound libraries (500 compounds) obtained from various marine organisms (bacteria, fungi, sponges)
- >14000 samples (crude extracts and fractions of pre-fractionated extracts) from marine micro-organisms (i.e., fungi, yeast, bacteria, algae) collected during the EU project PharmaSea. Most samples are stored as 10 mg/mL stocks (DMSO), others at different concentrations or solvent (percentage) or as dried stock.
SUPPORT FOR THE DEVELOPMENT OF ANTIBODY THERAPEUTICS
Provided to you by: EU-OPENSCREEN, EU-OPENSCREEN Partners & ERINHA
Due to the high demand in EU-OPENSCREEN services to support Diagnostic and Therapeutic Development, there is insufficient EC funding to provide you with our services at this time. Feel free to submit a pre-application to enter your research proposal into our list of potential future projects. They will be considered in received order, should additional funding become available in the future. Thank you very much for your understanding.
Contacts
EU-OPENSCREEN scientific-projects
scientific-projects@eu-openscreen.eu
Charlotte Wit
charlotte.wit@eu-openscreen.eu
All the services listed below are available for access regardless of the call for proposals & research topic that you select in your pre-application form. Services using replication-competent pathogens are indicated in the descriptions below along with the biosafety level. When applicable, fragments of pathogens are used (e.g., antibody discovery). For confirming the feasibility of your request, please contact us.
Library preparation
- VHH library preparation
Preparation of VHH libraries in phagmid vectors including pSEX81 and pMES4. Libraries from naive or immunized alpaca of very high efficiency.
Nanobody, antibody & antigen identification / engineering
- Nanobody identification
The service covers: - Protein overexpression in E. coli system (vector provided by applicant)
- Protein purification and verification by mass spectrometry
- Phage-display nanobody (VHH) library screen
- Verification of positive clones by ELISA test
- Nanobody sequence identification
- Training
- Antibody discovery and selection from B cells
Identification of antibodies from plasma of convalescent patients by B-cell cloning - Antigen or antibody design and engineering
Design and engineering of antibody with specific functions and suitable formats (IgG, Fab, single chain antibodies); engineering for increased stability, solubility, modulation of complement engagement, multi-specific constructs
Antibody and/or antigen production and characterization
- Antigen and/or antibody production, purification and characterization
Antibody and/or antigen production and purification, quality control of the samples, biophysical characterization (binding affinity, functionality, epitope mapping), in vitro neutralization assays - 3D structural models
3D structural analysis of antibodies, antigens and antibody-antigen complexes with experimentally guided computational simulations - Physico-chemical measurements of quality attributes
Structure, stability, aggregation (digital electrophoresis, DLS, CD, AUC, Multi Detector-AF4, SPR) - Assessment of endotoxin contamination
LAL tests
Evaluation of the selective antiviral activity of antibodies in virus-cell-based assays
3D structural models
3D structural analysis of antibodies, antigens and antibody-antigen complexes with experimentally guided computational simulations
VECTOR RESEARCH: HIGH-THROUGHPUT SCREENING SERVICES
provided to you by INFRAVEC
Contact
TNAManager@infravec2.eu
- Anopheles barcoded screen in vivo
- Standard Membrane Feeding Assay (SMFA) of live mosquitoes
SERVICES PROVIDED TO YOU BY: Transvac, VetBioNet & Instruct
Vaccine development requires a combination of specialized skills and technical capacities not readily available at a single organization. Find all those skills and capacities in our catalogue.
Please note that all in vivo models for studying immunogenicity, adjuvants or vaccine efficacy are available in the IN VIVO MODELS catalogue of services.
The services listed below are available for access regardless of the call for proposals and research topic you select in your pre-application form. When applicable, viral-like particles and/or pseudoviruses are used as study models for pathogens of interest.
VACCINE PLATFORM TECHNOLOGIES: SCREENING, EXPRESSION AND OPTIMISATION - currently not available
Provided to you by: Transvac & VetBioNet
Contacts
Catarina LUIS
Catarina.Luis@euvaccine.eu
William MARTIN
William.Martin@euvaccine.eu
- Cross-platform screening and pre‑clinical optimization with access to vaccine platform technologies (including proteins, viral like particles, viral vectors) and expression systems (including mammalian and insect cells)
Small-to-medium-scale (mg-scale) expression and purification of antigens from multiple candidate constructs. Expression can be compared in multiple expression systems, including P. pastoris, L. lactis, E. coli; Nicotiana; and constitutive/transient expression in mammalian/ insect cells. Vaccine formats include design and production of viral vector vaccines, Adenovirus (human and chimpanzee) and MVA - Custom construction of nanoparticles based on respiratory syncytial virus nucleoprotein as booster for antigen presentation
- Custom construction of recombinant viral proteins in HEK Freestyle cells
- Custom construction of recombinant vaccine
Two available backbones (non-deleted or E1-deleted genomes) derived from the Manhattan vaccine strain of the canine adenovirus type 2 (CAV-2) - Design and development of nanoparticle-based mucosal vaccine systems for SARS-CoV-2 or other respiratory pathogens
- Expression and purification of SARS-CoV structural proteins for vaccination and in vitro diagnostics
Expression systems available: E. coli, baculovirus
VACCINE PROCESS DEVELOPMENT & PRODUCTION - Currently not available
Provided to you by: Transvac*
Contacts
Catarina LUIS
Catarina.Luis@euvaccine.eu
William MARTIN
William.Martin@euvaccine.eu
- Pre‑clinical GLP production services
- Development and implementation of analytical methods for product characterization and process control and monitoring
- GMP manufacturing of starting materials
- GMP manufacturing of clinical materials
*Please note that ISIDORe funding may be limited for high cost GLP and GMP services, but might be provided as paid-for service
VACCINE ADJUVANTS & FORMULATION - currently not available
Provided to you by: Transvac
Contacts
Catarina LUIS
Catarina.Luis@euvaccine.eu
William MARTIN
William.Martin@euvaccine.eu
- Development and characterisation of vaccine formulations with liposomal adjuvants CAF01 and CAF09b
- Provision of CAF01 and CAF09b adjuvants at GMP grade for use in clinical studies
- Development and characterisation of vaccine formulations with adjuvants SWE, SQ, and SMQ and liposome adjuvants LQ and LMQ
- Upscaling of emulsion adjuvants (SQ, SMQ) and liposome adjuvants (LQ, LMQ) from lab-scale to pilot-scale prior to tech-transferto CDMO for GMP production
- Provision of SWE emulsion adjuvant at GMP grade for use in clinical studies
- Formulation and characterisation of vaccine candidates paired with mucosal or parenteral adjuvants.
STRUCTURAL & CHEMICAL CHARACTERIZATION OF VACCINES AND VACCINE ANTIGENS
Provided to you by: Instruct & the Joint Research Centre of the European Commission
Contact
Pauline AUDERGON
pauline@instruct-eric.org
- Structural characterisation of vaccine antigens (bound or unbound) – see also ANALYTICAL SERVICES
- X-ray methods
- From Sample to X-ray diffraction pipelines
- XChem Fragment Screening
- Online crystallography pipeline for Rapid structural characterization of antigens based on CrystalDirect technology
- Bio-SAXS, solution
- NMR technologies, solid state
- Atomic level characterization and/or interactions (IDP, proteins, host's proteins, nucleic acids, etc);
- Quality assurance via NMR (HOS of vaccines, antibodies, antigens/adjuvants);
- Fast fingerprinting/profiling via NMR metabolomics on blood (serum, plasma) and urine
- Fragment-screening by NMR
- Cryo-EM (single particle analysis)
- Scanning electron microscopy (SEM) -Transmission electron microscopy (TEM)
- Cryogenic electron microscopy (Cryo-EM)
- Electron tomography
- Cryo-ET (in combination with EuBi for correlative EM/light microscopy)
- X-ray methods
- Physico-chemical and in-vitro characterization of adjuvant and nanovaccines (such as LNP-mRNA)
Physical attributes (size distribution, particle concentration). Chemical (composition, free/bound cargo; cargo release kinetic); Stability (aggregation, time stability; mRNA/antigen integrity). In vitro toxicity (endotoxin contamination, cytotoxicity, immunotoxicity) - Identification and measurement of key quality attributes of nanovaccines
SERVICES Provided to you by BBMRI
Contact
Łukasz KOZERA
lukasz.kozera@bbmri-eric.eu
The services listed below are available for access only if you select a SARS-CoV-2 research topic
ACCESS TO EXISTING COLLECTIONS OF HUMAN CLINICAL SAMPLES – COVID 19 PATIENTS & CONTROLS
Includes datasets
Download description of available COVID 19 sample collections
Download description of available control sample collections
Download description of other viral infectious disease human sample collections
ON DEMAND COLLECTION OF HUMAN CLINICAL SAMPLES –COVID 19 PATIENTS & CONTROLS
ACCESS TO DATASETS COLLECTED TOGETHER WITH BIOLOGICAL SAMPLES
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ADVICE SERVICES
Provided to you by: EATRIS
Contact
David Morrow
davidmorrow@eatris.eu
You can access these services for all the open calls.
Regulatory oversight & advice
- Assessment of regulatory requirement for marketing authorization
- Scientific advice for preparing an application to the European Medicines Agency
- Informal scientific advice with selected national competent authorities, for highly complex projects
- Pre-clinical and clinical development plan development – Target Product Profile (TPP) and Investigational Medicinal Product Dossier (IMPD)
- Regulatory requirements for trial authorization and subsequent amendments by competent authorities and ethics committees, fast track procedures, coordinated authorization
Support for Clinical Trials
Provided to you by: ECRIN
Contact
Sara RAZA KHAN
sara.raza-khan@ecrin.org
If you are a researcher, principal investigator or Sponsor, reach out to ECRIN for assistance in planning and design of your clinical research proposals. Please note that these services do not encompass the operational costs of conducting a clinical trial.
Protocol Design For Clinical Trials
- Support for clinical trial methodology, selection of trial design, endpoints and core outcome measures
Planning For clinical trials
- Planning of clinical trial operations, including regulatory / ethical requirements, informed consent, data monitoring plan, data management and data sharing plan
- Supporting the development of the main aspects of funding applications including grant proposals and preparation of trial budget
- Support in identifying available funding mechanisms
- Advice on strategies for site selection and patient recruitment
- Task distribution for multinational study management
Open access tools (www.ecrin.org/tools)
ACCESS TO EUROPEAN CLINICAL TRIALS [CLOSED]
Provided to you by: ECRIN
Contact
Sara RAZA KHAN
sara.raza-khan@ecrin.org
Access to ongoing platform trials for new therapeutic, prevention or vaccine intervention arms (Only for SARS-COV-2/COVID-19)
This service offers to conduct clinical trials as new intervention arms in one of the three EU-funded adaptive platform trials (including operational management services such as regulatory/ethical submission of protocol amendments, IMP management, pharmacovigilance, data management, monitoring):
- REMAP‑COVID (also known as REMAP-CAP), an international platform trial for CAP (community acquired pneumonia) initiated in 2014 and rapidly expanded to include COVID-19 patients. Several domains of this trial are exclusive for patients with confirmed or suspected COVID-19.
- EU‑SolidAct a pan-European adaptive platform trial involved with rapid and coordinated investigation of new and repurposed medications to treat Covid-19 in hospitalized patients.
- VACCELERATE (European Corona Vaccine Trial Accelerator Platform), will accelerate phase 2 & 3 COVID-19 vaccine trials.
If you need support for your research on other pathogens with epidemic or pandemic potential such as orthopoxviruses, polio & non polio enteroviruses, or pathogen X, please contact us.
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Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Immunological assays (ELISA, Flow cytometry)
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Lung | |
| Nose | |
| Blood vessel | |
| Liver | |
| Kidney | |
| Brain | |
| 3D tissue and cell printer | |
| Animal | |
| Lung | Cattle |
| Intestinal | Cattle, Chicken |
Air Liquid Interface (ALI) polarised cells
| Human | |
| Lung | |
| Airway nasal | |
| Airway tracheal | |
| Airway bronchial | |
| CALU-3 | |
| A549 | |
| RPMI-2650 | |
| Animal | |
| Lung | Cattle, Chicken, Pig |
| Airway nasal | Sheep, Pig |
| Airway tracheal | Sheep, Pig, Mouse |
| Airway bronchial | Sheep, Pig |
| Intestinal | Cattle, Chicken |
Primary cells
| Human | |
| Immune cells ( macrophages, dendritic cells) | |
| Lung | |
| Cultures from surgical specimens | |
| Animal | |
| Immune cells (monocytes, macrophages, lymphocytes, dendritic cells) | Cattle, Sheep, Pig |
| Lung | Cattle, Sheep, Bat |
| Bronchial | Pig |
| Intestine | Bat |
Tissue section cultures
| Human | |
| Placental precision-cut slices | |
| Animal | |
| Lung Precision Cut slices | Mouse, Hamster, Pig, Sheep, Cattle, |
| Liver Precision Cut slices | Sheep |
Organotypic cultures
| Animal | |
| Lung | Chicken, Ferret, Pig |
| Trachea | Chicken, Ferret, Pig |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| HTR-8 | |
| RPMI-2650 | |
| HEPA-RG | |
| Nasal cell line | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
| Lung | Chicken |
| Bronchial | Pig |
Stem cells
| Human | |
| Mesenchymal | |
| Redifferentiated IPSCS (Induced pluripotent stem cells) | |
| Animal | |
| Mesenchymal | Cattle, Sheep, Pig, Mink, Rabbit |
Engineered cells
| Animal | |
| VERO HSLAM ((Human) signaling lymphocytic activation molecule) | African Green Monkey |
| VERO E6 with fluorescent viability reporter gene (m-Cherry-H2B (Histone-2B) Protein) | African Green Monkey |
Other
Custom cell requests may be considered.
| Human | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| Animal | |
| Preparation of tissues | Mammalian and Avian tissues |
| Preparation of little organs for clearing (Lungs) with I and U DISCO | Mouse |
Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Blood vessel | |
| Liver | |
| Kidney |
Air Liquid Interface (ALI) polarised cells
| Human | |
| A549 |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
Engineered cells
| Human | |
| HUH-7 expressing EBOV VP30 | |
| HUH-7 expressing MARV VP30 | |
| HUH-7 expressing SUDV VP30 | |
| A549 expressing EBOV VP30 | |
| A549 expressing MARV VP30 | |
| A549 expressing SUDV VP30 | |
| Animal | |
| VERO E6 expressing EBOV VP30 | African Green Monkey |
| VERO E6 expressing MARV VP30 | African Green Monkey |
| VERO E6 expressing SUDV VP30 | African Green Monkey |
Other
Custom cell requests may be considered.
| Human | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| Animal | |
| Preparation of tissues | Mammalian and Avian tissues |
All the services listed below are available for access regardless of the call for proposals and research topic that you select in your pre-application form.
SOCIAL SCIENCES SERVICES
Provided to you by: Sonar-Global
Contact
Sarah Marsh ARNAUD
sarah.arnaud@pasteur.fr
Social sciences preparedness and response interventions
- Vulnerability assessments
This service provides ethnographic investigation of locally-defined case definitions of social groups most likely to be marginalized or excluded before or during an epidemic; offer systematic analysis of complex factors leading to or aggravating marginalization - Protocols & implementation for public engagement, acceptability and compliance with epidemic control efforts: clinical trials, nonpharmaceutical interventions, and vaccination
This service will develop protocols for assessing the public engagement, acceptability and compliance with control efforts of targeted measures and if needed, support the implementation of these protocols
Post-intervention evaluation
- Intervention or response evaluation
Evaluation of the planning, development and implementation of specific epidemic intervention or response (including for COVID-19 pandemic) - Ethical evaluation: post-intervention assessment of ethical stakes at country level in West and Central Africa.
Service available for West and Central Africa French-speaking countries.
Evaluation of ethical dimensions/consequences of an intervention, (including and specific to the COVID-19 pandemic): Socio-anthropological assessment based on enquiries with national and local authorities, communities, teams and participants in the project. Offers assessment of social effects of program. Service is available for West and Central Africa French-speaking countries. - Ethical evaluation: Ethical assessment of program/intervention (elsewhere)
Evaluation of ethical dimensions/consequences of an intervention, (including and specific to the COVID-19 pandemic): Ethical evaluation of program or intervention by trained and experienced bioethics team
Scale-up services for qualitative analyses and epidemic response
- Demographic, health, socio-economic data and analyses
Scaling up of existing qualitative analyses to demographic, health and socio-economic data and analyses - Policy analysis
Systematic review of local policy measures and synthesis of key lessons learnt to inform scale-up in preparedness and ongoing response
Cost benefit analysis of epidemic response measure
- Cost benefit analysis of epidemic response measure
Evaluation of costs and benefits associated with public health intervention (including COVID-19), resulting in a report to be delivered at end of service
Community surveillance and social dimensions of outbreak investigation
- Design of community surveillance activities for human and animal health, to complement existing surveillance systems
Develop an adapted, locally appropriate plan for community detection of outbreaks of new COVID-19 waves. This service would enable local public health authorities to identify social risks and to facilitate community engagement and participation in the identification of these risks. Where appropriate, this plan will include human interactions with potential animal reservoirs in which COVID-19 has been detected. Rapid quantitative and qualitative methods, including key informant interviews and targeted focus group discussions will be employed - Design, implementation and supervision of community surveillance activities for human and animal health, to complement existing surveillance systems
Develop an adapted, locally appropriate plan for community detection of outbreaks of new COVID-19 waves. This service would enable local public health authorities to identify social risks and to facilitate community engagement and participation in the identification of these risks. Where appropriate, this plan will include human interactions with potential animal reservoirs in which COVID-19 has been detected. Rapid quantitative and qualitative methods, including key informant interviews and targeted focus group discussions will be employed - Development of protocol of social sciences community investigation of human/animal disease outbreak
This service will offer the development of a protocol to investigate the social dimensions of new outbreaks that may involve spill overs from animals into human beings (as well as spillbacks). The service will provide understanding of specific social, cultural and livelihood dimensions of human-animal interactions as well as concrete recommendations for prevention - Development and implementation of protocol of social sciences community investigation of human/animal disease outbreak
This service will offer the development and implementation of a protocol to investigate the social dimensions of new outbreaks that may involve spill overs from animals into human beings (as well as spillbacks). The service will provide understanding of specific social, cultural and livelihood dimensions of human-animal interactions as well as concrete recommendations for prevention
SERVICES FOR DISEASE VECTOR SURVEILLANCE
Provided to you by: Emergen & INFRAVEC
Contact
sequencing-services@isidore-project.eu
Sequencing services on disease surveillance can be found here.
- Vector field site access and training
- Spacial modelling
FieldWork
Provided to you by: INFRAVEC
Contact
TNAManager@infravec2.eu
Vector fieldwork Services
Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Immunological assays (ELISA, Flow cytometry)
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Lung | |
| Nose | |
| Blood vessel | |
| Liver | |
| Kidney | |
| Brain | |
| Animal | |
| Lung | Cattle, Sheep, Pig |
Air Liquid Interface (ALI) polarised cells
| Human | |
| Lung | |
| Airway nasal | |
| Airway tracheal | |
| Airway bronchial | |
| CALU-3 | |
| A549 | |
| Animal | |
| Lung | Cattle, Chicken |
| Airway nasal | Sheep |
| Airway tracheal | Sheep, Mouse |
| Airway bronchial | Sheep |
Primary cells
| Human | |
| Immune cells ( macrophages, dendritic cells) | |
| Cultures from surgical specimens (Rift valley fever virus model) | |
| Animal | |
| Immune cells (monocytes, macrophages, lymphocytes, dendritic cells) | Cattle, Sheep, Pig |
| Lung | Cattle, Bat |
| Bronchial | Pig |
| Intestine | Bat |
| Hepatocytes | Sheep |
| Maternal epithelial cells | Sheep |
| Umbilical cord derived endothelial cells | Sheep |
| Kidney | Chicken |
Tissue section cultures
| Human | |
| Lung precision-cut slices | |
| Placental precision-cut slices | |
| Animal | |
| Lung precision-cut slices | Mouse, Hamster, Pig, Sheep, Cattle, Chicken |
| Liver precision-cut slices | Sheep |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| HTR-8 | |
| BeWO | |
| HEPA-RG (Rift Valley fever virus model) | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
| Lung | Chicken |
| UMNSAH/DF-1 | Chicken |
| Bronchial | Pig |
| Neuro-2a | Mouse |
| C6/36 | Aedes albopictus |
| Aag2 | Aedes aegypti |
Stem cells
| Human | |
| Mesenchymal | |
| Animal | |
| Mesenchymal | Sheep |
Other
Custom cell requests may be considered.
| Human | |
| Neuronal/Glial cells | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| 3D-vessel-on-a-chip | |
| Animal | |
| Transplacental model (maternal epithelial cells and trophoblasts) | Sheep |
| 3D-vessel-on-a-chip | |
| Preparation of tissues | Mammalian and Avian tissues |
Structural Biology Services
Provided to you by instruct
Contact
Pauline AUDERGON
isidore@instruct-eric.org
The services listed below are available for access regardless of the call for proposals and research topic you select in your pre-application form.
Nanobody discovery
- Generation and characterisation of conformational nanobodies (to facilitate the structural analysis of proteins that are notoriously difficult to purify, to crystallize or to study by another method.)
- Rapid selection of nanobodies by screening/affinity maturation
Crystallography
- Crystallisation of Proteins and Nucleic Acids
- High-throughput Crystallisation
- CrystalDirect Online Crystallography protein-to-structure pipeline
- IceBear crystallography data management (data management, crystallization, data collection)
ISIDORe Services in action:
Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. doi.org/10.1038/s41467-020-17495-9
Protein production for Structural Biology
- Protein expression
- Cloning
- High throughput expression
- Protein purification
- Biomolecular complex purification
Molecular Biophysics
Wide range of techniques to study the biophysical characterization of the structure, function and stability of biological macromolecules like proteins, nucleic acids, lipids and their complexes; as well as the kinetic and thermodynamic parameters of their interaction.
- Circular Dichroism
- Differential Scanning Fluorescence
- Differential Scanning Calorimetry
- Dynamic Light Scattering
- UV/Vis Spectrometry
- Microscale Thermophoresis
- Surface Plasmon Resonance,
- High Throughput Biolayer Interferometry
- Isothermal titration Calorimetry
- Antibody screening in patient sera (Robotein automated Bimolecular analysis platform)
- SEC-MALS (multi-angle light scattering)
ISIDORe Services in action:
Poor antibody response to BioNTech/Pfizer COVID-19 vaccination in SARS-CoV-2 naïve residents of nursing homes. doi:10.1093/cid/ciab998
Single Molecule and Super-Resolution Microscopy for Structural Biology applications (Instruct)
- Single-molecule detection with fluorescence microscopy techniques: using widefield microscopy such as TIRF, super-resolution methods SMLM (STORM, GSD/GSDIM, PALM, PAINT)
Mass Spectrometry
- Native mass spectrometry
- Single cell mass spectrometry
- Proteomic mass spectrometry with possibility for plasma proteome analysis including monitoring of viral and immune response proteins, analysis of single viral proteins and binding to drugs and antibodies
- Glycan analysis by Mass spectrometry
- GC-MS for the analysis of cuticle thickness to test insecticide resistance in mosquitoes
ISIDORe Services in action:
ICAM-1 induced re-arrangements of capsid and genome prime rhinovirus 14 for activation and uncoating. doi.org/10.1073/pnas.2024251118
Electron Microscopy techniques for Structural Biology
- Scanning electron microscopy (SEM)
- Transmission electron microscopy (TEM)
- Cryogenic electron microscopy (Cryo-EM)
- Electron Microscopy Data Processing Services
- Electron tomography
- Cryo-Electron tomography
- Cryo-Correlative Light and EM
ISIDORe Services in action:
Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects macaques from infection. doi: 10.1016/j.xcrm.2022.100528
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. doi: 10.1126/science.abd5223
Magnetic Resonance Techniques
- Solution NMR
- Solid state NMR
- Fragment-screening by NMR
- NMR metabolomic
- NMR-based screening of protein-drug interactions
- Glycan analysis by NMR
ISIDORe Services in action:
The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a. doi: 10.1126/sciadv.abm4034
In-Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells. doi:10.1002/anie.202007184
X Ray Structural Biology Techniques
- X-ray crystallography
- Biological small angle scattering (Bio-SAXS),
- X-ray imaging from synchrotron sources
- XChem Fragment Screening
ISIDORe Services in action:
The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a. doi: 10.1126/sciadv.abm4034.
PDB-REDO
Procedure to optimise crystallographic structure models, providing algorithms that make a fully automated decision-making system for refinement, rebuilding and validation.
- PDB-REDO
AlphaFill
AlphaFold models enriched with ligands and co-factors.
- Alphafill
IMAGING SERVICES
Provided to you by Euro-BioImaging ERIC & VetBioNet
Contact
Arina RYBINA info@eurobioimaging.eu
How imaging technologies contribute to understanding viruses
Imaging technologies used to understand COVID-19 infection
Imaging techniques and COVID19 diagnosis
Understanding SARS-CoV-2 replication cycle in human cells
All the services listed below are available for access at BSL-1 or BSL-2 regardless of the call for proposals & research topic that you select in your pre-application form.
Preparation of samples at BSL3 might be accommodated as part of the service.
Imaging services that can be provided directly in BSL-3 containment are marked with an *
Light Microscopy & Advanced Light Microscopy for Biological Imaging
Fluorescence microscopy
- Laser scanning confocal microscopy (LSCM/CLSM)
- Spinning disc confocal microscopy (SDCM)*
- Light sheet microscopy (LSM) and lattice light sheet microscopy (LLSM)
- Structured illumination microscopy (SIM)
- Widefield microscopy: Total internal reflection fluorescence microscopy (TIRF)
- Deconvolution widefield microscopy (DWM)*
- Image scanning microscopy
- Two-Photon Microscopy/Multi-photon microscopy systems
Fluorescence Nanoscopy
- Stimulated Emission Depletion Microscopy (STED)
- Single-molecule localisation microscopy techniques (SMLM): STORM, GSD/GSDIM, PALM
- Reversible optical fluorescence transitions (RESOLFT)
- Super-resolution localization microscopy – localization super-resolution experiments (SMLM: dSTORM, GSDIM, STORM, PALM, PAINT), particle tracking, standard wide-field epifluorescence and TIRF microscopy, transmission microscopy.
- MINFLUX
Functional Imaging and Specialized Technologies
- High-throughput microscopy (HTM)/High content screening (HCS), RNAi screens
- Protein dynamics and interactions (FRET, FCS, FCCS, FLIM, FRAP)
- Multi-photon microscopy
- High resolution episcopic microscopy (HREM)
- Photomanipulation
- High speed imaging
- Feedback microscopy
- Cryo-FM
Mesoscopic Imaging
- Light Sheet mesoscopic imaging: Single-plane illumination microscopy (SPIM), dSLSM
- Optical projection tomography (OPT)
Label-free Imaging
- Quantitative phase imaging (QPI)
- Raman spectroscopy
- Coherent Anti-Stokes Raman Scattering microscopy (CARS)
ISIDORe Services in action
3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations. doi:10.1093/bioinformatics/bty200. Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera
doi: 10.1002/bies.202000257
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003
Virus morphology: Insights from super-resolution fluorescence microscopy
doi: 10.1016/j.csbj.2021.10.038
Sample Characterization
- Atomic force microscopy (AFM)
- MSI - Mass Spectrometry - based Imaging
Electron microscopy for Biological Imaging / Ultrastructural Analysis in 2D & 3D
- Scanning electron microscopy (SEM), including 3D SEM of plastic embedded samples
- Array tomography
- Focused-ion-beam scanning EM (FIB-SEM)
- Serial Block Face Scanning EM (SBF-SEM or SBEM)
- Transmission Electron Microscopy, including Serial section TEM (ssTEM)
- TEM tomography, STEM tomography
- Cryogenic electron Microscopy (Cryo-EM: Cryo-ET, Cryo-SEM, Cryo-FIB, Cryo-TEM)
- Immuno-electron microscopy (immunogold labelling of Tokuyasu cryosections)
ISIDORe Services in action
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003
SARS-CoV-2 infection induces the dedifferentiation of multiciliated cells and impairs mucociliary clearance doi.org/10.1038/s41467-021-24521-x
Correlative Light Microscopy & Electron Microscopy for Biological Imaging
- CLEM from live cells to plastic sections ("live" CLEM)
- Correlative light-electron microscopy from live cells to 3D plastic embedded samples
- Intravital CLEM
- High accuracy on section CLEM
- CLEM on Tokuyasu sections
- CryoCLEM
ISIDORe Services in action
Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies doi.org/10.1038/s42003-020-01567-z
Phase contrast X-Ray Imaging
- Phase contrast X ray imaging (PCI)
ISIDORe Services in action
3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography doi: 10.7554/eLife.60408
Animal imaging (multimodal imaging of small animals)
- Multimodal imaging of small animals
- In vivo optical imaging
- Intravital microscopy
- Magnetic Resonance Imaging (MRI)
- Ultra-sound imaging (US)
- Computed tomography (CT)
- Nuclear imaging (PET, SPECT)
- Bimodal technologies
- Provision of imaging probes/tracers
Animal Monitoring
- Animal behaviour monitoring
- Quantitative spatial-temporal monitoring of individual animals and groups using TrackLab or EthoVision XT software (computer vision, UWB, GPS sensors)
- Computer-aided monitoring: Registration and analysis of manual observations of animals directly or with video feeds/films, potentially including synchronization of data streams, e.g., of physiology by means of The Observer XT
- Animal physiology monitoring
- Body temperature (combined with other variables as required), physiology sensors dependent on the animal species and variables required
Histopathology
- Histopathology
Image Data & Image Analysis
- Biological and Bio-Medical Image data analysis, including consultation and development of novel analysis and visualisation solutions
- AI and Machine Learning (ML)
- Medical Image Data Archiving
ISIDORe Services in action
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003
Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera doi: 10.1002/bies.202000257
Sequencing SERVICES
Provided to you by Emergen & INFRAVEC
Contacts
sequencing-services@isidore-project.eu
The services listed below are available for access regardless of the call for proposals and research topic you select in your pre-application form.
** These services can be provided in combination with or without bioinformatics support.
Genomic sequencing services (BACTERial / viral DNA / RNA genome)
- Illumina technology**
- Oxford Nanopore technology
- Bacterial Genome Sequencing
ISIDORe Services in action
Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075
Metagenome sequencing services
- Shotgun metagenome sequencing (AP-HP CHU Henri Mondor Technologie patent and accreditation): identification of any microorganism (up to 100/week)
- Viral metagenome sequencing: identification of any virus (up to 100/week)
- 16S rRNA metagenome sequencing
- Pan-pathogen surveillance through shotgun metagenomics
ISIDORe Services in action
Identification of necrotizing dermohypodermitis and fasciitis causative microbial agents and microbiota by targeted and shotgun metagenomics
doi: 10.1111/bjd.18611
Inclusion-Body Encephalitis Detected and Characterized by Standardized and Validated Shotgun Metagenomic Approach
doi: 10.3201/eid2609.200366
Fatal Encephalitis Caused by Cristoli virus, a New Emerging Member of the Orthobunyavirus genus of the Peribunyaviridae family
doi: 10.3201/eid2606.191431
Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms
doi: 10.3390/microorganisms8101539
Metagenomic Investigation of Torque Teno Mini Virus-SH in Hematological Patients
doi: 10.3389/fmicb.2019.01898
Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management
doi:10.3390/v10110633
Quality Control Implementation for Universal Characterization of DNA and RNA Viruses in Clinical Respiratory Samples Using Single Metagenomic Next-Generation Sequencing Workflow
doi:10.1186/s12879-018-3446-5
Metatranscriptome sequencing services
- Viral metatranscriptomic – Whole genome sequencing of RNA viruses, including SARS-CoV-2 (up to 100 /week)
ISIDORe Services in action
Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075
Miscellaneous sequencing services
- Small RNA Illumina sequencing**
- Long read DNA sequencing by Nanopore**
- RNAseq total transcriptome Illumina sequencing**
- Genotyping of mosquitoes, insecticide resistance and detection of pathogens
ISIDORe Services in action
Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075
Respiratory pathogens (non-SARS-CoV-2)
Coronaviridae, Orthomyxoviridae, etc.
Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Immunological assays (ELISA, Flow cytometry)
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Lung | |
| Nose | |
| Blood vessel | |
| Liver | |
| Kidney | |
| Brain | |
| 3D tissue and cell printer | |
| Animal | |
| Lung | Pig |
Air Liquid Interface (ALI) polarised cells
| Human | |
| Lung | |
| Airway nasal | |
| Airway tracheal | |
| Airway bronchial | |
| CALU-3 | |
| A549 | |
| Animal | |
| Airway nasal | Sheep |
| Airway tracheal | Sheep, Mouse |
| Airway bronchial | Sheep |
Primary cells
| Human | |
| Immune cells (macrophages, dendritic cells) | |
| Animal | |
| Immune cells (monocytes, macrophages, lymphocytes, dendritic cells) | Cattle, Sheep, Pig |
| Bronchial | Pig |
| Lung | Bat |
| Intestine | Bat |
| Kidney (Avian infectious bronchitis virus model) | Chicken |
| Embryo Kidney (Avian Influenza model) | Chicken |
Tissue section cultures
| Human | |
| Lung precision-cut slices | |
| Placental precision-cut slices | |
| Animal | |
| Lung precision-cut slices | Mouse, Hamster, Pig, Sheep, Cattle, Chicken |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| HTR-8 | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
| DF1 Embryonal fibroblasts | Chicken |
Stem cells
| Human | |
| Mesenchymal | |
| Animal | |
| Mesenchymal | Cattle, Sheep, Pig, Mink, Rabbit |
Engineered cells
| Animal | |
| VERO HSLAM ((Human) signaling lymphocytic activation molecule) | African Green Monkey |
Other
Custom cell requests may be considered.
| Human | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| Animal | |
| Embryonated Specific Pathogen Free Eggs (Avian Influenza model) | Chicken |
| Preparation of tissues | Mammalian and Avian tissues |
Cell model - immortalised cell lines
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Vero E6
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability (incl. high content imaging)
- Bioimaging/Microscopy (incl. high content imaging)
- Flow cytometry
- Immunohistochemistry
- Histological methods
Vero CCL81
- Virus isolation
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR (E, RdRP, N, S)
- Omics - spatial transcriptomics
- Sequencing - NGS
- ELISA (N)
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
- Flow cytometry
- Luminex assay for antibody detection
- Histopathology
- Immunohistochemistry
- Histological methods
Calu 3
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
- Flow cytometry
- Immunohistochemistry
- Histological methods
A549
- Virus titration
- Neutralization assay
- Cytotoxicity
- Antiviral assay
- CPE (TCID50)
- qRT-PCR
- Immunofluorescence
- Cell viability (incl. high content imaging)
- Bioimaging/Microscopy ((conventional - high resolution confocal microscopy ; high content imaging)
Caco-2
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
MDCK
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Hep-2
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Huh-7
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
RPMI-2650
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
human nasal cell line
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Chicken lung epithelial cells
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR - primer sets for chicken innate immune genes)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Pig bronchial epithelial cells
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Cell model - primary cells
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
pig macrophages
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
pig monocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
pig lymphocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
sheep monocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
sheep macrophages (monocyte-derived)
- Virus titration
- Neutralization assay
- Antiviral assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
sheep macrophages (alveolar)
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
sheep macrosheep lymphocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
human primary epithelial lung cells (monolayers/polarised 2D culture)
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
bovine primary epithelial lung cells (monolayers/polarised 2D culture)
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
ovine primary epithelial lung cells (monolayers/polarised 2D culture)
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
cattle macrophages (monocyte-derived)
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
cattle macrophages (alveolar)
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
primary human cell cultures from surgical specimens
- Virus isolation
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Bat lung epithelial cells
- Virus isolation
- Virus titration
- Antiviral assay
- CPE (TCID50)
- qRT-PCR (E, RdRP, N, S)
- Sequencing - NGS
- ELISA (N)
- Immunofluorescence
- Luminex assay for antibody detection
- Histopathology
Bat intestine epithelial cells
- Virus isolation
- Virus titration
- Antiviral assay
- CPE (TCID50)
- qRT-PCR (E, RdRP, N, S)
- Sequencing - NGS
- ELISA (N)
- Immunofluorescence
- Luminex assay for antibody detection
- Histopathology
Swine bronchial epithelial cells
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR )
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Cell model - mesenchymal stem cells
Provided to you by VetBioNet, ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
rabbit mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
mink mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
bovine mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
pig mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
Cell model - Well differentiated and/or polarised cell systems
Provided to you by VetBioNet, ERINHA & EMBRC
Contact
exvivo-invivo-services@isidore-project.eu
ALI-differentiated 2D culture of primary human lung cells
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
ALI-differentiated 2D culture of primary bovine lung cells
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Calu-3 differentiated in ALI conditions
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
A549 differentiated in ALI conditions
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Chicken lung epithelial cells - ALI
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR - primer sets for chicken innate immune genes)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Pig bronchial epithelial cells - ALI
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
RPMI-2650 in ALI 2D cultures
- Vi
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Non-conventional screening models for toxicity and ecotoxicity
Non-conventional screening models for toxicity and ecotoxicity assays:
- zebrafish eggs: up to 48h, 96 well format
- invertebrates (rotifers and artemia): 96 well format
- microalgae
Cell model - Engineered cell lines and primary cells
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Vero hSLAM ((human) signaling lymphocytic activation molecule)
- Virus isolation
- Virus titration
- Neutralization assay
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
- Histopathology
- Immunohistochemistry
- In situ hybridization
Vero E6 with fluorescent viability reporter gene (m-cherry-H2B (histon-2B) protein)
- Cytotoxicity (combined with high-content imaging)
- Cell viability (high-content imaging)
- Bioimaging/Microscopy (high-content imaging)
redifferentiated iPSCs (induced Pluripotent Stem Cells)
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Cell model - Other 2D cell model
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Preparation of mammalian tissues
- Cloning (Cell sorting on plates - 96, 384…)
- Immunofluorescence (conventional and confocal microscopy)
- Bioimaging / microscopy (conventional and confocal microscopy)
- Flow cytometry (multicolor flow cytometry, High Speed cell sorting)
- Histopathology (histology / immunochemistry)
Preparation of avian tissues
- Cloning (Cell sorting on plates - 96, 384…)
- Immunofluorescence (conventional and confocal microscopy)
- Bioimaging / microscopy (conventional and confocal microscopy)
- Flow cytometry (multicolor flow cytometry, High Speed cell sorting)
- Histopathology (histology / immunochemistry)
Swab / saliva collection devices
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Cell model - Organoids
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
human lung organoids
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
bovine lung organoids
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
3D tissue and cell printer
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Cell model - Precision-cut tissue slices cultures
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Bovine lung PCLS (Precision Cut Lung Slices)
- qRT-PCR (Fluidigm medium-throughput qPCR - primer sets for >200 bovine genes, mainly related to immunity)
- ELISA (IL-8; IL-1b,…..)
- Immunofluorescence (confocal microscopy)
- Cell viability (LDH release assay)
Hamster PC lung tissue
- Virus isolation
- Virus titration
- Neutralization assay
- Typing
- Omics - transcriptomic analysis by nanostring assay
- Sequencing - NGS
- Histopathology (incl. Immunohistology)
Sheep primary lung PCLS
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
Cattle primary lung PCLS
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
Mouse primary lung PCLS
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
Cell model - Organotypic culture
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Chicken tracheal culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Chicken lung culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Ferret tracheal culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Ferret lung culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Pig tracheal culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Pig lung culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Cell model - Other 3D cell models
Preparation of little organs for clearing (lung of mouse) with i and u DISCO
- Cloning (Cell sorting on plates - 96, 384…)
- Immunofluorescence (conventional and confocal microscopy)
- Bioimaging / microscopy (conventional and confocal microscopy)
- Flow cytometry (multicolor flow cytometry, High Speed cell sorting)
- Histopathology (histology / immunochemistry)
SERVICES PROVIDED TO YOU BY: VetBioNet, Transvac, Infrafrontier, ERINHA & EMBRC
ISIDORe will only offer access to in vivo models in the absence of adequate alternative methods to achieve an identical result (REPLACE). Please do not forget to check out our wide range of EX VIVO MODELS.
When in vivo models cannot be substituted with any other comparable method, we will use the smallest number necessary for quality science (REDUCE), as well as state-of-the-art practices to protect animal welfare and prevent animal pain and distress (REFINE).
Positively evaluated requests for access to in vivo models will be subjected to institutional ethical evaluation before any implementation can happen.
The services listed below are a general overview of ISIDORe’s in vivo capacities. Models are not available for all species and/or all pathogens. If you want to make sure that we can provide access to your model of interest, please contact us: exvivo-invivo-services@isidore-project.eu
MODELS FOR INFECTION STUDIES
Please note that agents from the Plasmodiidae and Trypanosomatidae famililes can only be studied in Arthropods. Main exceptions are indicated in brackets. Other specific exceptions may apply.
Provided to you by: VetBioNet, Infrafrontier & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse1
- Hamster (available for RG4 pathogens)
- Guinea Pig (not available for vector-borne pathogens)
- Rabbit
- Ferret
- Pig1,3
- Sheep5 (not available for RG4 pathogens)
- Cattle (not available for RG4 pathogens)
- Non-human primates
- Livestock
- Camelids (not available for RG4 pathogens)
- Chicken2 (not available for RG4 pathogens)
- Fruitbats (not available for RG4 pathogens)
- Wildlife2,4 (not available for RG4 pathogens)
- Zebrafish (not available for RG4 pathogens)
- Arthropods (Only available for vector-borne pathogens)
1 Includes models expressing human ACE2
2 Includes avian influenza models
3 Includes pig influenza models
4 Includes vector-transmission models
5 Includes pregnant sheep models
MODELS FOR DRUG EFFICACY STUDIES
Please note that agents from the Plasmodiidae and Trypanosomatidae famililes can only be studied in Arthropods. Main exceptions are indicated in brackets. Other specific exceptions may apply.
Provided to you by: VetBioNet, Infrafrontier & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse1
- Hamster (not available for RG4 pathogens)
- Guinea Pig (not available for vector-borne pathogens)
- Rabbit
- Ferret
- Pig1,3
- Sheep5 (not available for RG4 pathogens)
- Cattle (not available for RG4 pathogens)
- Non-human primates
- Livestock
- Camelids (not available for RG4 pathogens)
- Chicken2 (not available for RG4 pathogens)
- Fruitbats (not available for RG4 pathogens)
- Wildlife2,4 (not available for RG4 pathogens)
- Zebrafish (not available for RG4 pathogens)
- Arthropods (Only available for vector-borne pathogens)
1 Includes models expressing human ACE2
2 Includes avian influenza models
3 Includes pig influenza models
4 Includes vector-transmission models
5 Includes pregnant sheep models
MODELS FOR VACCINE EFFICACY STUDIES
Please note that agents from the Plasmodiidae and Trypanosomatidae famililes can only be studied in Arthropods. Main exceptions are indicated in brackets. Other specific exceptions may apply.
Provided to you by: VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse1
- Hamster (not available for RG4 pathogens)
- Guinea Pig (not available for vector-borne pathogens)
- Rabbit
- Ferret
- Pig1,3
- Sheep5 (not available for RG4 pathogens)
- Cattle (not available for RG4 pathogens)
- Non-human primates
- Livestock
- Camelids (not available for RG4 pathogens)
- Chicken2 (not available for RG4 pathogens)
- Fruitbats (not available for RG4 pathogens)
- Wildlife2,4 (not available for RG4 pathogens)
- Zebrafish (not available for RG4 pathogens)
- Arthropods (Only available for vector-borne pathogens)
1 Includes models expressing human ACE2
2 Includes avian influenza models
3 Includes pig influenza models
4 Includes vector-transmission models
5 Includes pregnant sheep models
MODELS FOR VACCINE IMMUNOGENICITY STUDIES
Provided to you by: VetBioNet, Transvac & EMBRC
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse
- Hamster
- Rabbit
- Ferret
- Pig
- Sheep
- Cattle
- Non-human primates
- Camelids
- Chicken
- Wildlife Zebrafish
MODELS FOR VECTOR RESEARCH
All of the vectors listed below can be provided free of pathogens. Some of the vectors listed below are provided ONLY free of pathogens and are marked with an *. If you want to make sure that we can provide access to your vector of interest, please contact us.
Provided to you by: INFRAVEC
Contact
TNAManager@infravec2.eu
| Aedes spp | (available pathogen-free and carrying members of the Flaviviridae, Togaviridae & Trypanosomatidae1 families) |
| Anopheles spp | (available pathogen-free and carrying members of the Flaviviridae and Plasmodiidae families) |
| Culex spp | (available pathogen-free and carrying members of the Flaviridae family) |
| Culocoides spp* | (avalaible pathogen-free only) |
| Glossina spp* | (avalaible pathogen-free only) |
| Hyalomma spp* | (avalaible pathogen-free only) |
| Lutzomyia spp | (available pathogen-free and carrying members of the Trypanosomatidae1 family) |
| Ornithodoros spp* | (avalaible pathogen-free only) |
| Phlebotomus spp | (available pathogen-free and carrying members of the Trypanosomatidae1 family) |
| Rhipicephalus spp* | (avalaible pathogen-free only) |
| Sergentomyia spp | (available pathogen-free and carrying members of the Trypanosomatidae1 family) |
| Stomoxys spp* | (avalaible pathogen-free only) |
Mosquito mass rearing* (up to 1000, 10 000, 100 000 specimens) may be available under request.
1 including Leishmania
GENERATION OF NEW STUDY MODELS FOR SARS-CoV-2 RESEARCH
Provided to you by: Infrafrontier
Contact
Asrar Ali KHAN
asrar.khan@infrafrontier.eu
- Generation of precision mouse models
- Humanization of mouse model cohorts by AAV-driven hACE2 expression
- Generation of knock-out mice (service starting 2023)
- Generation of knock-in mice (service starting 2023)
DETECTION & CHARACTERIZATION OF IMMUNE TISSUES & CELLS
Provided to you by: EATRIS, VetBioNet, Infrafrontier & ERINHA
Contact
Patricia Carvajal-Vallejos
patriciacarvajal@eatris.eu
- Immune-function profiling
This service is available for access regardless of the call for proposals and research topic that you select in your pre-application form. Antigen-specific T proliferation and cytokine, chemokine and immune factor analysis (mass cytometry, FACSCanto, LSR IV, Symphony, Helios, Bio-Plex Multiplex immunoassay). - Immune-cell profiling
This service is available for access in the following calls for proposals: CALL I (SARS-CoV-2), CALL IV (non-SARS-CoV-2 respiratory pathogens), CALL V (vector-borne pathogens), and CALL VI (Other epidemic-prone pathogens). - Antiviral screening & mucosal immunology
This service is available for access for SARS-CoV-2 research projects. Including human airway models for testing drugs and for virus – cells interaction, to evaluate the role of individual immune subsets in different contexts against infectious disease and to characterize viral isolates. - Detection and quantification of SARS-CoV-2-specific T cells at the single cell level
This service is available for access for SARS-CoV-2 and MPXV research projects - T-cell cloning and expansion
This service is available for access for SARS-CoV-2 research projects. Determination of specificity - Detection and quantification of SARS-CoV-2-specific B cells at the single cell level
This service is available for access for SARS-CoV-2 research projects. - Access to organoids, spheroids & multifluidic devices for immune surveillance (IncuCyte live-cell imaging of spheroids)
This service is available for access for SARS-CoV-2 research projects.- Virus sequencing, non-coding RNA expression and antibody responses to viral antigens with high-content imaging and analysis.
- Access to Multi-site Immuno-analysis of SARS-CoV-2, including analysis of infected samples based on metal tag detection by mass cytometry
DETECTION & CHARACTERIZATION OF THE IMMUNE RESPONSE
Provided to you by: EATRIS, VetBioNet & ERINHA
Contact
Patricia Carvajal-Vallejos
patriciacarvajal@eatris.eu
- Medium‑ to large-scale analysis of immune proteins
The services listed below are available for access for SARS-CoV-2 research projects.- Protein/peptide identification
- Antibody Characterization / Multi-Attribute Method (MAM)
- Post-Translational Modifications Analysis (Glycosylation; Oxidation/Deamination, Glycan Identity)
- High-throughput Quantitative Proteomics – SWATH analysis (untargeted; relative quantification)
- Intact Protein Measurement
- Aggregation and refolding (SEC chromatography)
- Antibody profiling to evaluate the host immune response
- ICS-T-cell-responses (TRM), Virus-immunome profiling
Quantification of cytokines/chemokines (Bio-plex Multiplex Immunoassay), surface and intracellular detection of markers/cytokines (flow cytometry) in infected biological samples - Functional studies of pathogenicity of genetic variants at molecular and cellular level
Including virus sequencing, non-coding RNAs expression and ELISA assay, drugs; drug testing - Epigenetics of immune cells
To study genome-wide epigenetic changes including DNA methylation, histone modifications and non-coding RNAs expression - Immunoprofiling in swine and poultry
Polychromatic flow cytometry assays, single cell immunomics, MHC haplotyping, Luminex cytokine profiling
DETECTION, CHARACTERIZATION & MODULATION OF IMMUNE GENE EXPRESSION
Provided to you by: EATRIS & VetBioNet
Contact
exvivo-invivo-services@isidore-project.eu
The services listed below are available for access regardless of the call for proposals and research topic that you select in your pre-application form.
- siRNA libraries
- Human
- Swine
- Poultry
- sgRNA/CRISPR Cas9 knockout libraries
- Human
- Swine
- Poultry
- Cattle
- RNAseq transcriptomics, 16S NGS microbiome analysis, metabolomics (LC-MS) in livestock
- Swine
- Poultry
- Specific primer sets and protocols for medium-throughput Fluidigm qPCR targeting up to 96 immune genes
- Mice
- Swine
- Cattle
- Chicken
BIO IMAGING FOR IMMUNO PROFILING
Provided to you by: Euro-BioImaging
Contact
info@eurobioimaging.eu
All the services listed below are available for access at BSL-1 or BSL-2 regardless of the call for proposals & topic you select.
- Development and validation of imaging probes
Targeting of specific molecular inflammation markers or subpopulations of immune cells in surrogate infection models in vivo - Biomedical imaging technologies for monitoring the immune system
- PET
- MRI
- CT
- US
- Optical imaging
- Multimodal imaging
- High-throughput Imaging & Bioimage Analysis
PerkinElmer Opera Phenix & Molecular Devices ImageXpress Nano. Automation for sample processing and Imaging in both +37 C and RT. Image analysis pipelines and customized solutions for DNN based segmentation & classification in 2D and 3D.
SUPPORT FOR THE DEVELOPMENT OF DIAGNOSTICS
Provided to you by the Biomedical Research Foundation, Academy of Athens (BRFAA), the Joanneum Research (JR), and Joint Research Center of European Commission (JRC) in collaboration with EU-OPENSCREEN
Due to the high demand in EU-OPENSCREEN services to support Diagnostic and Therapeutic Development, there is insufficient EC funding to provide you with our services at this time. Feel free to submit a pre-application to enter your research proposal into our list of potential future projects. They will be considered in received order, should additional funding become available in the future. Thank you very much for your understanding.
Contact
EU-OPENSCREEN scientific-projects
scientific-projects@eu-openscreen.eu
Charlotte Wit
charlotte.wit@eu-openscreen.eu
All the services listed below are available for access at BSL-1 or BSL-2 regardless of the call for proposals & research topic that you select in your pre-application form:
- Characterization of in-vitro diagnostic devices and sensing platforms
Electron microscopy (SEM-EDX, TEM-EDX); Surface analysis (XPS, TOF-SIMS); Raman Microscope; Array scanner - Assay development (molecular and biochemical) and integration to IVD devices
Customization of existing assays to be integrated into LoCs, biosensors and microfluidics-based devices - Testing of developed and optimized assays, biosensors, LoCs and microfluidics-based devices with well-characterized samples
Extensive biobank of blood & nasopharyngeal samples from patients infected with various viral and bacterial pathogens. - Surface functionalization
Development of surface modification techniques towards biomolecule immobilization and biosensor fabrication or tailoring of surface properties (antifouling, surface energy etc.) - Lab-on-a-Chip molecular diagnostics, multiplexed pathogen detection, variant discrimination
- Lab-on-a-chip design
Simulation-based fluidics design for existing assays - Lab-on-a-chip implementation
Implementation and adaptation of existing assays into foil-based lab-on-chip - Lab-on-a-chip demonstrator
Foil-based lab-on-chip demonstrator device development for existing assays - Matrix customized methods (e.g., non-human samples) and multiplexed pathogen detection
Development/application of rapid, low cost, high throughput molecular methods for population screening
VECTOR MONITORING
Provided to you by INFRAVEC
Contact
TNA Manager
TNAManager@infravec2.eu
Personalized training in the development and application of molecular diagnostics for vector monitoring
Personalized (1-2 people) laboratory training in state-of-the art molecular biology laboratories to develop and apply molecular diagnostics relevant for modern vector monitoring.
Once you have submitted the ISIDORe pre-application below, please complete the Full application for access to this Personalized Training.
Access to the personnal training application
SUPPORT FOR THE DEVELOPMENT OF SMALL MOLECULE THERAPEUTICS
Provided to you by: EU-OPENSCREEN, EU-OPENSCREEN Partners, ERINHA & EMBRC
Due to the high demand in EU-OPENSCREEN services to support Diagnostic and Therapeutic Development, there is insufficient EC funding to provide you with our services at this time. Feel free to submit a pre-application to enter your research proposal into our list of potential future projects. They will be considered in received order, should additional funding become available in the future. Thank you very much for your understanding.
Contacts
EU-OPENSCREEN scientific-projects
scientific-projects@eu-openscreen.eu
Charlotte Wit
charlotte.wit@eu-openscreen.eu
All the services listed below are available for access regardless of the call for proposals & research topic that you select in your pre-application form. The maximum biosafety level of containment for the performance of the experiments is indicated in the description of the services. For confirming the feasibility of your request, please contact us.
Small molecule libraries – provided ONLY in combination with high throughput screening (HTS) services offered below
- Repurposing Library
Preparation of assay-ready plates with drug repurposing libraries containing approved and clinical trial compounds - European Chemical Biology Library (ECBL)
Preparation of assay-ready plates with 100.000 small molecules containing approx. 2464 bioactives - EU-OPENSCREEN Fragment Library
Preparation of plates with approx. 1000 fragments including 88 minifrags - EU-OPENSCREEN Bioactives
Preparation of plates with 2464 bioactives
Assay development, high throughput screening and hit profiling services for identification of active small molecule and host-targeting agents
- Assay development
Assay design and development in a broad range of readouts including phenotypic assays in BSL2-BSL3 facilities (bacterial growth inhibition and viral infection inhibition, cell-based HCS, host cell response), and BSL1 in-vitro target-based assays with specific bacterial, viral and human targets - Biochemical and enzymatic target-based high-throughput screening
High-throughput screening using BSL1 in-vitro target-based assays with specific bacterial, viral and human targets. The assay needs to be HTS-compatible with demonstrated performance in 384-well format. The service includes assay transfer, HTS and hit validation
Do not forget to request library if necessary. - Cell-based high-throughput screening
Cell-based screen including phenotypic, and target-based that can be run in both, human and bacterial, cells in BSL2 facilities. The assay needs to be HTS-compatible with demonstrated performance in 384-well format. The service includes assay transfer, HTS and hit validation
Do not forget to request library if necessary - Low- and medium-throughput screening in BSL3 facilities
Cell-based screen including phenotypic, and target-based that can be run in human cells and pathogen infection models in BSL3 facilities. The service includes assay transfer, screening and hit validation - Fragment screening
Includes assay development, screening and hit validation - Hit validation and profiling
Disease-relevant models, ADMET, ROS‑tox and others
ISIDORe Services in action
The blood-brain barrier is dysregulated in COVId-19 and serves as a CNS entry route for SARS-CoV-2 doi.org/10.1016/j.stemcr.2021.12.011
Characterization of ACE Inhibitors and AT1R Antagonists with Regard to Their Effect on ACE2 Expression and Infection with SARS-CoV-2 Using a Caco-2 Cell Model
doi.org/10.3390/life11080810
X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease
doi: 10.1126/science.abf7945
Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen
doi.org/10.1021/acsptsci.0c00216
A SARS-CoV-2 cytopathicity dataset generated by high-content screening of a large drug repurposing collection
doi.org/10.1038/s41597-021-00848-4
EVALUATION OF THE SELECTIVE ANTIVIRAL ACTIVITY OF AGENTS IN VIRUS-CELL-BASED ASSAYS
Medicinal chemistry support
- Drug design & evaluation in silico
- Hit-to-lead development following HTS of small molecules
- Fragment-to-lead development fragment screening
- Optimization of potency, selectivity and in vitro/in vivo ADMET properties of small molecule drug candidates
- Design and synthesis of target degraders (PROTACs, RIBOTACs)
Natural compound libraries
provided by EMBRC
Contact
Davide Di Cioccio
davide.dicioccio@embrc.eu
- Natural compound libraries (500 compounds) obtained from various marine organisms (bacteria, fungi, sponges)
- >14000 samples (crude extracts and fractions of pre-fractionated extracts) from marine micro-organisms (i.e., fungi, yeast, bacteria, algae) collected during the EU project PharmaSea. Most samples are stored as 10 mg/mL stocks (DMSO), others at different concentrations or solvent (percentage) or as dried stock.
SUPPORT FOR THE DEVELOPMENT OF ANTIBODY THERAPEUTICS
Provided to you by: EU-OPENSCREEN, EU-OPENSCREEN Partners & ERINHA
Due to the high demand in EU-OPENSCREEN services to support Diagnostic and Therapeutic Development, there is insufficient EC funding to provide you with our services at this time. Feel free to submit a pre-application to enter your research proposal into our list of potential future projects. They will be considered in received order, should additional funding become available in the future. Thank you very much for your understanding.
Contacts
EU-OPENSCREEN scientific-projects
scientific-projects@eu-openscreen.eu
Charlotte Wit
charlotte.wit@eu-openscreen.eu
All the services listed below are available for access regardless of the call for proposals & research topic that you select in your pre-application form. Services using replication-competent pathogens are indicated in the descriptions below along with the biosafety level. When applicable, fragments of pathogens are used (e.g., antibody discovery). For confirming the feasibility of your request, please contact us.
Library preparation
- VHH library preparation
Preparation of VHH libraries in phagmid vectors including pSEX81 and pMES4. Libraries from naive or immunized alpaca of very high efficiency.
Nanobody, antibody & antigen identification / engineering
- Nanobody identification
The service covers: - Protein overexpression in E. coli system (vector provided by applicant)
- Protein purification and verification by mass spectrometry
- Phage-display nanobody (VHH) library screen
- Verification of positive clones by ELISA test
- Nanobody sequence identification
- Training
- Antibody discovery and selection from B cells
Identification of antibodies from plasma of convalescent patients by B-cell cloning - Antigen or antibody design and engineering
Design and engineering of antibody with specific functions and suitable formats (IgG, Fab, single chain antibodies); engineering for increased stability, solubility, modulation of complement engagement, multi-specific constructs
Antibody and/or antigen production and characterization
- Antigen and/or antibody production, purification and characterization
Antibody and/or antigen production and purification, quality control of the samples, biophysical characterization (binding affinity, functionality, epitope mapping), in vitro neutralization assays - 3D structural models
3D structural analysis of antibodies, antigens and antibody-antigen complexes with experimentally guided computational simulations - Physico-chemical measurements of quality attributes
Structure, stability, aggregation (digital electrophoresis, DLS, CD, AUC, Multi Detector-AF4, SPR) - Assessment of endotoxin contamination
LAL tests
Evaluation of the selective antiviral activity of antibodies in virus-cell-based assays
3D structural models
3D structural analysis of antibodies, antigens and antibody-antigen complexes with experimentally guided computational simulations
VECTOR RESEARCH: HIGH-THROUGHPUT SCREENING SERVICES
provided to you by INFRAVEC
Contact
TNAManager@infravec2.eu
- Anopheles barcoded screen in vivo
- Standard Membrane Feeding Assay (SMFA) of live mosquitoes
SERVICES PROVIDED TO YOU BY: Transvac, VetBioNet & Instruct
Vaccine development requires a combination of specialized skills and technical capacities not readily available at a single organization. Find all those skills and capacities in our catalogue.
Please note that all in vivo models for studying immunogenicity, adjuvants or vaccine efficacy are available in the IN VIVO MODELS catalogue of services.
The services listed below are available for access regardless of the call for proposals and research topic you select in your pre-application form. When applicable, viral-like particles and/or pseudoviruses are used as study models for pathogens of interest.
VACCINE PLATFORM TECHNOLOGIES: SCREENING, EXPRESSION AND OPTIMISATION - currently not available
Provided to you by: Transvac & VetBioNet
Contacts
Catarina LUIS
Catarina.Luis@euvaccine.eu
William MARTIN
William.Martin@euvaccine.eu
- Cross-platform screening and pre‑clinical optimization with access to vaccine platform technologies (including proteins, viral like particles, viral vectors) and expression systems (including mammalian and insect cells)
Small-to-medium-scale (mg-scale) expression and purification of antigens from multiple candidate constructs. Expression can be compared in multiple expression systems, including P. pastoris, L. lactis, E. coli; Nicotiana; and constitutive/transient expression in mammalian/ insect cells. Vaccine formats include design and production of viral vector vaccines, Adenovirus (human and chimpanzee) and MVA - Custom construction of nanoparticles based on respiratory syncytial virus nucleoprotein as booster for antigen presentation
- Custom construction of recombinant viral proteins in HEK Freestyle cells
- Custom construction of recombinant vaccine
Two available backbones (non-deleted or E1-deleted genomes) derived from the Manhattan vaccine strain of the canine adenovirus type 2 (CAV-2) - Design and development of nanoparticle-based mucosal vaccine systems for SARS-CoV-2 or other respiratory pathogens
- Expression and purification of SARS-CoV structural proteins for vaccination and in vitro diagnostics
Expression systems available: E. coli, baculovirus
VACCINE PROCESS DEVELOPMENT & PRODUCTION - Currently not available
Provided to you by: Transvac*
Contacts
Catarina LUIS
Catarina.Luis@euvaccine.eu
William MARTIN
William.Martin@euvaccine.eu
- Pre‑clinical GLP production services
- Development and implementation of analytical methods for product characterization and process control and monitoring
- GMP manufacturing of starting materials
- GMP manufacturing of clinical materials
*Please note that ISIDORe funding may be limited for high cost GLP and GMP services, but might be provided as paid-for service
VACCINE ADJUVANTS & FORMULATION - currently not available
Provided to you by: Transvac
Contacts
Catarina LUIS
Catarina.Luis@euvaccine.eu
William MARTIN
William.Martin@euvaccine.eu
- Development and characterisation of vaccine formulations with liposomal adjuvants CAF01 and CAF09b
- Provision of CAF01 and CAF09b adjuvants at GMP grade for use in clinical studies
- Development and characterisation of vaccine formulations with adjuvants SWE, SQ, and SMQ and liposome adjuvants LQ and LMQ
- Upscaling of emulsion adjuvants (SQ, SMQ) and liposome adjuvants (LQ, LMQ) from lab-scale to pilot-scale prior to tech-transferto CDMO for GMP production
- Provision of SWE emulsion adjuvant at GMP grade for use in clinical studies
- Formulation and characterisation of vaccine candidates paired with mucosal or parenteral adjuvants.
STRUCTURAL & CHEMICAL CHARACTERIZATION OF VACCINES AND VACCINE ANTIGENS
Provided to you by: Instruct & the Joint Research Centre of the European Commission
Contact
Pauline AUDERGON
pauline@instruct-eric.org
- Structural characterisation of vaccine antigens (bound or unbound) – see also ANALYTICAL SERVICES
- X-ray methods
- From Sample to X-ray diffraction pipelines
- XChem Fragment Screening
- Online crystallography pipeline for Rapid structural characterization of antigens based on CrystalDirect technology
- Bio-SAXS, solution
- NMR technologies, solid state
- Atomic level characterization and/or interactions (IDP, proteins, host's proteins, nucleic acids, etc);
- Quality assurance via NMR (HOS of vaccines, antibodies, antigens/adjuvants);
- Fast fingerprinting/profiling via NMR metabolomics on blood (serum, plasma) and urine
- Fragment-screening by NMR
- Cryo-EM (single particle analysis)
- Scanning electron microscopy (SEM) -Transmission electron microscopy (TEM)
- Cryogenic electron microscopy (Cryo-EM)
- Electron tomography
- Cryo-ET (in combination with EuBi for correlative EM/light microscopy)
- X-ray methods
- Physico-chemical and in-vitro characterization of adjuvant and nanovaccines (such as LNP-mRNA)
Physical attributes (size distribution, particle concentration). Chemical (composition, free/bound cargo; cargo release kinetic); Stability (aggregation, time stability; mRNA/antigen integrity). In vitro toxicity (endotoxin contamination, cytotoxicity, immunotoxicity) - Identification and measurement of key quality attributes of nanovaccines
SERVICES Provided to you by BBMRI
Contact
Łukasz KOZERA
lukasz.kozera@bbmri-eric.eu
The services listed below are available for access only if you select a SARS-CoV-2 research topic
ACCESS TO EXISTING COLLECTIONS OF HUMAN CLINICAL SAMPLES – COVID 19 PATIENTS & CONTROLS
Includes datasets
Download description of available COVID 19 sample collections
Download description of available control sample collections
Download description of other viral infectious disease human sample collections
ON DEMAND COLLECTION OF HUMAN CLINICAL SAMPLES –COVID 19 PATIENTS & CONTROLS
ACCESS TO DATASETS COLLECTED TOGETHER WITH BIOLOGICAL SAMPLES
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ADVICE SERVICES
Provided to you by: EATRIS
Contact
David Morrow
davidmorrow@eatris.eu
You can access these services for all the open calls.
Regulatory oversight & advice
- Assessment of regulatory requirement for marketing authorization
- Scientific advice for preparing an application to the European Medicines Agency
- Informal scientific advice with selected national competent authorities, for highly complex projects
- Pre-clinical and clinical development plan development – Target Product Profile (TPP) and Investigational Medicinal Product Dossier (IMPD)
- Regulatory requirements for trial authorization and subsequent amendments by competent authorities and ethics committees, fast track procedures, coordinated authorization
Support for Clinical Trials
Provided to you by: ECRIN
Contact
Sara RAZA KHAN
sara.raza-khan@ecrin.org
If you are a researcher, principal investigator or Sponsor, reach out to ECRIN for assistance in planning and design of your clinical research proposals. Please note that these services do not encompass the operational costs of conducting a clinical trial.
Protocol Design For Clinical Trials
- Support for clinical trial methodology, selection of trial design, endpoints and core outcome measures
Planning For clinical trials
- Planning of clinical trial operations, including regulatory / ethical requirements, informed consent, data monitoring plan, data management and data sharing plan
- Supporting the development of the main aspects of funding applications including grant proposals and preparation of trial budget
- Support in identifying available funding mechanisms
- Advice on strategies for site selection and patient recruitment
- Task distribution for multinational study management
Open access tools (www.ecrin.org/tools)
ACCESS TO EUROPEAN CLINICAL TRIALS [CLOSED]
Provided to you by: ECRIN
Contact
Sara RAZA KHAN
sara.raza-khan@ecrin.org
Access to ongoing platform trials for new therapeutic, prevention or vaccine intervention arms (Only for SARS-COV-2/COVID-19)
This service offers to conduct clinical trials as new intervention arms in one of the three EU-funded adaptive platform trials (including operational management services such as regulatory/ethical submission of protocol amendments, IMP management, pharmacovigilance, data management, monitoring):
- REMAP‑COVID (also known as REMAP-CAP), an international platform trial for CAP (community acquired pneumonia) initiated in 2014 and rapidly expanded to include COVID-19 patients. Several domains of this trial are exclusive for patients with confirmed or suspected COVID-19.
- EU‑SolidAct a pan-European adaptive platform trial involved with rapid and coordinated investigation of new and repurposed medications to treat Covid-19 in hospitalized patients.
- VACCELERATE (European Corona Vaccine Trial Accelerator Platform), will accelerate phase 2 & 3 COVID-19 vaccine trials.
If you need support for your research on other pathogens with epidemic or pandemic potential such as orthopoxviruses, polio & non polio enteroviruses, or pathogen X, please contact us.
[post_title] => SUSPENDED: Other [post_excerpt] => [post_status] => publish [comment_status] => closed [ping_status] => closed [post_password] => [post_name] => other [to_ping] => [pinged] => [post_modified] => 2024-09-10 18:22:44 [post_modified_gmt] => 2024-09-10 15:22:44 [post_content_filtered] => [post_parent] => 334 [guid] => https://isidore-project.eu/?post_type=services&p=952 [menu_order] => 5 [post_type] => services [post_mime_type] => [comment_count] => 0 [filter] => raw ) )SUSPENDED: Cell models for research
PROVIDED BY VetBioNet, ERINHA & EMBRC
Browse our extensive range of 2D & 3D models for characterizing infections & choose the best option for your research
SUSPENDED: SARS-CoV-2SUSPENDED: Risk Group 4 PathogensSUSPENDED: Vector-borne pathogensSUSPENDED: Respiratory pathogensSUSPENDED: OtherArray
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Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Immunological assays (ELISA, Flow cytometry)
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Lung | |
| Nose | |
| Blood vessel | |
| Liver | |
| Kidney | |
| Brain | |
| 3D tissue and cell printer | |
| Animal | |
| Lung | Cattle |
| Intestinal | Cattle, Chicken |
Air Liquid Interface (ALI) polarised cells
| Human | |
| Lung | |
| Airway nasal | |
| Airway tracheal | |
| Airway bronchial | |
| CALU-3 | |
| A549 | |
| RPMI-2650 | |
| Animal | |
| Lung | Cattle, Chicken, Pig |
| Airway nasal | Sheep, Pig |
| Airway tracheal | Sheep, Pig, Mouse |
| Airway bronchial | Sheep, Pig |
| Intestinal | Cattle, Chicken |
Primary cells
| Human | |
| Immune cells ( macrophages, dendritic cells) | |
| Lung | |
| Cultures from surgical specimens | |
| Animal | |
| Immune cells (monocytes, macrophages, lymphocytes, dendritic cells) | Cattle, Sheep, Pig |
| Lung | Cattle, Sheep, Bat |
| Bronchial | Pig |
| Intestine | Bat |
Tissue section cultures
| Human | |
| Placental precision-cut slices | |
| Animal | |
| Lung Precision Cut slices | Mouse, Hamster, Pig, Sheep, Cattle, |
| Liver Precision Cut slices | Sheep |
Organotypic cultures
| Animal | |
| Lung | Chicken, Ferret, Pig |
| Trachea | Chicken, Ferret, Pig |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| HTR-8 | |
| RPMI-2650 | |
| HEPA-RG | |
| Nasal cell line | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
| Lung | Chicken |
| Bronchial | Pig |
Stem cells
| Human | |
| Mesenchymal | |
| Redifferentiated IPSCS (Induced pluripotent stem cells) | |
| Animal | |
| Mesenchymal | Cattle, Sheep, Pig, Mink, Rabbit |
Engineered cells
| Animal | |
| VERO HSLAM ((Human) signaling lymphocytic activation molecule) | African Green Monkey |
| VERO E6 with fluorescent viability reporter gene (m-Cherry-H2B (Histone-2B) Protein) | African Green Monkey |
Other
Custom cell requests may be considered.
| Human | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| Animal | |
| Preparation of tissues | Mammalian and Avian tissues |
| Preparation of little organs for clearing (Lungs) with I and U DISCO | Mouse |
Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Blood vessel | |
| Liver | |
| Kidney |
Air Liquid Interface (ALI) polarised cells
| Human | |
| A549 |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
Engineered cells
| Human | |
| HUH-7 expressing EBOV VP30 | |
| HUH-7 expressing MARV VP30 | |
| HUH-7 expressing SUDV VP30 | |
| A549 expressing EBOV VP30 | |
| A549 expressing MARV VP30 | |
| A549 expressing SUDV VP30 | |
| Animal | |
| VERO E6 expressing EBOV VP30 | African Green Monkey |
| VERO E6 expressing MARV VP30 | African Green Monkey |
| VERO E6 expressing SUDV VP30 | African Green Monkey |
Other
Custom cell requests may be considered.
| Human | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| Animal | |
| Preparation of tissues | Mammalian and Avian tissues |
All the services listed below are available for access regardless of the call for proposals and research topic that you select in your pre-application form.
SOCIAL SCIENCES SERVICES
Provided to you by: Sonar-Global
Contact
Sarah Marsh ARNAUD
sarah.arnaud@pasteur.fr
Social sciences preparedness and response interventions
- Vulnerability assessments
This service provides ethnographic investigation of locally-defined case definitions of social groups most likely to be marginalized or excluded before or during an epidemic; offer systematic analysis of complex factors leading to or aggravating marginalization - Protocols & implementation for public engagement, acceptability and compliance with epidemic control efforts: clinical trials, nonpharmaceutical interventions, and vaccination
This service will develop protocols for assessing the public engagement, acceptability and compliance with control efforts of targeted measures and if needed, support the implementation of these protocols
Post-intervention evaluation
- Intervention or response evaluation
Evaluation of the planning, development and implementation of specific epidemic intervention or response (including for COVID-19 pandemic) - Ethical evaluation: post-intervention assessment of ethical stakes at country level in West and Central Africa.
Service available for West and Central Africa French-speaking countries.
Evaluation of ethical dimensions/consequences of an intervention, (including and specific to the COVID-19 pandemic): Socio-anthropological assessment based on enquiries with national and local authorities, communities, teams and participants in the project. Offers assessment of social effects of program. Service is available for West and Central Africa French-speaking countries. - Ethical evaluation: Ethical assessment of program/intervention (elsewhere)
Evaluation of ethical dimensions/consequences of an intervention, (including and specific to the COVID-19 pandemic): Ethical evaluation of program or intervention by trained and experienced bioethics team
Scale-up services for qualitative analyses and epidemic response
- Demographic, health, socio-economic data and analyses
Scaling up of existing qualitative analyses to demographic, health and socio-economic data and analyses - Policy analysis
Systematic review of local policy measures and synthesis of key lessons learnt to inform scale-up in preparedness and ongoing response
Cost benefit analysis of epidemic response measure
- Cost benefit analysis of epidemic response measure
Evaluation of costs and benefits associated with public health intervention (including COVID-19), resulting in a report to be delivered at end of service
Community surveillance and social dimensions of outbreak investigation
- Design of community surveillance activities for human and animal health, to complement existing surveillance systems
Develop an adapted, locally appropriate plan for community detection of outbreaks of new COVID-19 waves. This service would enable local public health authorities to identify social risks and to facilitate community engagement and participation in the identification of these risks. Where appropriate, this plan will include human interactions with potential animal reservoirs in which COVID-19 has been detected. Rapid quantitative and qualitative methods, including key informant interviews and targeted focus group discussions will be employed - Design, implementation and supervision of community surveillance activities for human and animal health, to complement existing surveillance systems
Develop an adapted, locally appropriate plan for community detection of outbreaks of new COVID-19 waves. This service would enable local public health authorities to identify social risks and to facilitate community engagement and participation in the identification of these risks. Where appropriate, this plan will include human interactions with potential animal reservoirs in which COVID-19 has been detected. Rapid quantitative and qualitative methods, including key informant interviews and targeted focus group discussions will be employed - Development of protocol of social sciences community investigation of human/animal disease outbreak
This service will offer the development of a protocol to investigate the social dimensions of new outbreaks that may involve spill overs from animals into human beings (as well as spillbacks). The service will provide understanding of specific social, cultural and livelihood dimensions of human-animal interactions as well as concrete recommendations for prevention - Development and implementation of protocol of social sciences community investigation of human/animal disease outbreak
This service will offer the development and implementation of a protocol to investigate the social dimensions of new outbreaks that may involve spill overs from animals into human beings (as well as spillbacks). The service will provide understanding of specific social, cultural and livelihood dimensions of human-animal interactions as well as concrete recommendations for prevention
SERVICES FOR DISEASE VECTOR SURVEILLANCE
Provided to you by: Emergen & INFRAVEC
Contact
sequencing-services@isidore-project.eu
Sequencing services on disease surveillance can be found here.
- Vector field site access and training
- Spacial modelling
FieldWork
Provided to you by: INFRAVEC
Contact
TNAManager@infravec2.eu
Vector fieldwork Services
Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Immunological assays (ELISA, Flow cytometry)
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Lung | |
| Nose | |
| Blood vessel | |
| Liver | |
| Kidney | |
| Brain | |
| Animal | |
| Lung | Cattle, Sheep, Pig |
Air Liquid Interface (ALI) polarised cells
| Human | |
| Lung | |
| Airway nasal | |
| Airway tracheal | |
| Airway bronchial | |
| CALU-3 | |
| A549 | |
| Animal | |
| Lung | Cattle, Chicken |
| Airway nasal | Sheep |
| Airway tracheal | Sheep, Mouse |
| Airway bronchial | Sheep |
Primary cells
| Human | |
| Immune cells ( macrophages, dendritic cells) | |
| Cultures from surgical specimens (Rift valley fever virus model) | |
| Animal | |
| Immune cells (monocytes, macrophages, lymphocytes, dendritic cells) | Cattle, Sheep, Pig |
| Lung | Cattle, Bat |
| Bronchial | Pig |
| Intestine | Bat |
| Hepatocytes | Sheep |
| Maternal epithelial cells | Sheep |
| Umbilical cord derived endothelial cells | Sheep |
| Kidney | Chicken |
Tissue section cultures
| Human | |
| Lung precision-cut slices | |
| Placental precision-cut slices | |
| Animal | |
| Lung precision-cut slices | Mouse, Hamster, Pig, Sheep, Cattle, Chicken |
| Liver precision-cut slices | Sheep |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| HTR-8 | |
| BeWO | |
| HEPA-RG (Rift Valley fever virus model) | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
| Lung | Chicken |
| UMNSAH/DF-1 | Chicken |
| Bronchial | Pig |
| Neuro-2a | Mouse |
| C6/36 | Aedes albopictus |
| Aag2 | Aedes aegypti |
Stem cells
| Human | |
| Mesenchymal | |
| Animal | |
| Mesenchymal | Sheep |
Other
Custom cell requests may be considered.
| Human | |
| Neuronal/Glial cells | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| 3D-vessel-on-a-chip | |
| Animal | |
| Transplacental model (maternal epithelial cells and trophoblasts) | Sheep |
| 3D-vessel-on-a-chip | |
| Preparation of tissues | Mammalian and Avian tissues |
Structural Biology Services
Provided to you by instruct
Contact
Pauline AUDERGON
isidore@instruct-eric.org
The services listed below are available for access regardless of the call for proposals and research topic you select in your pre-application form.
Nanobody discovery
- Generation and characterisation of conformational nanobodies (to facilitate the structural analysis of proteins that are notoriously difficult to purify, to crystallize or to study by another method.)
- Rapid selection of nanobodies by screening/affinity maturation
Crystallography
- Crystallisation of Proteins and Nucleic Acids
- High-throughput Crystallisation
- CrystalDirect Online Crystallography protein-to-structure pipeline
- IceBear crystallography data management (data management, crystallization, data collection)
ISIDORe Services in action:
Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. doi.org/10.1038/s41467-020-17495-9
Protein production for Structural Biology
- Protein expression
- Cloning
- High throughput expression
- Protein purification
- Biomolecular complex purification
Molecular Biophysics
Wide range of techniques to study the biophysical characterization of the structure, function and stability of biological macromolecules like proteins, nucleic acids, lipids and their complexes; as well as the kinetic and thermodynamic parameters of their interaction.
- Circular Dichroism
- Differential Scanning Fluorescence
- Differential Scanning Calorimetry
- Dynamic Light Scattering
- UV/Vis Spectrometry
- Microscale Thermophoresis
- Surface Plasmon Resonance,
- High Throughput Biolayer Interferometry
- Isothermal titration Calorimetry
- Antibody screening in patient sera (Robotein automated Bimolecular analysis platform)
- SEC-MALS (multi-angle light scattering)
ISIDORe Services in action:
Poor antibody response to BioNTech/Pfizer COVID-19 vaccination in SARS-CoV-2 naïve residents of nursing homes. doi:10.1093/cid/ciab998
Single Molecule and Super-Resolution Microscopy for Structural Biology applications (Instruct)
- Single-molecule detection with fluorescence microscopy techniques: using widefield microscopy such as TIRF, super-resolution methods SMLM (STORM, GSD/GSDIM, PALM, PAINT)
Mass Spectrometry
- Native mass spectrometry
- Single cell mass spectrometry
- Proteomic mass spectrometry with possibility for plasma proteome analysis including monitoring of viral and immune response proteins, analysis of single viral proteins and binding to drugs and antibodies
- Glycan analysis by Mass spectrometry
- GC-MS for the analysis of cuticle thickness to test insecticide resistance in mosquitoes
ISIDORe Services in action:
ICAM-1 induced re-arrangements of capsid and genome prime rhinovirus 14 for activation and uncoating. doi.org/10.1073/pnas.2024251118
Electron Microscopy techniques for Structural Biology
- Scanning electron microscopy (SEM)
- Transmission electron microscopy (TEM)
- Cryogenic electron microscopy (Cryo-EM)
- Electron Microscopy Data Processing Services
- Electron tomography
- Cryo-Electron tomography
- Cryo-Correlative Light and EM
ISIDORe Services in action:
Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects macaques from infection. doi: 10.1016/j.xcrm.2022.100528
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. doi: 10.1126/science.abd5223
Magnetic Resonance Techniques
- Solution NMR
- Solid state NMR
- Fragment-screening by NMR
- NMR metabolomic
- NMR-based screening of protein-drug interactions
- Glycan analysis by NMR
ISIDORe Services in action:
The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a. doi: 10.1126/sciadv.abm4034
In-Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells. doi:10.1002/anie.202007184
X Ray Structural Biology Techniques
- X-ray crystallography
- Biological small angle scattering (Bio-SAXS),
- X-ray imaging from synchrotron sources
- XChem Fragment Screening
ISIDORe Services in action:
The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a. doi: 10.1126/sciadv.abm4034.
PDB-REDO
Procedure to optimise crystallographic structure models, providing algorithms that make a fully automated decision-making system for refinement, rebuilding and validation.
- PDB-REDO
AlphaFill
AlphaFold models enriched with ligands and co-factors.
- Alphafill
IMAGING SERVICES
Provided to you by Euro-BioImaging ERIC & VetBioNet
Contact
Arina RYBINA info@eurobioimaging.eu
How imaging technologies contribute to understanding viruses
Imaging technologies used to understand COVID-19 infection
Imaging techniques and COVID19 diagnosis
Understanding SARS-CoV-2 replication cycle in human cells
All the services listed below are available for access at BSL-1 or BSL-2 regardless of the call for proposals & research topic that you select in your pre-application form.
Preparation of samples at BSL3 might be accommodated as part of the service.
Imaging services that can be provided directly in BSL-3 containment are marked with an *
Light Microscopy & Advanced Light Microscopy for Biological Imaging
Fluorescence microscopy
- Laser scanning confocal microscopy (LSCM/CLSM)
- Spinning disc confocal microscopy (SDCM)*
- Light sheet microscopy (LSM) and lattice light sheet microscopy (LLSM)
- Structured illumination microscopy (SIM)
- Widefield microscopy: Total internal reflection fluorescence microscopy (TIRF)
- Deconvolution widefield microscopy (DWM)*
- Image scanning microscopy
- Two-Photon Microscopy/Multi-photon microscopy systems
Fluorescence Nanoscopy
- Stimulated Emission Depletion Microscopy (STED)
- Single-molecule localisation microscopy techniques (SMLM): STORM, GSD/GSDIM, PALM
- Reversible optical fluorescence transitions (RESOLFT)
- Super-resolution localization microscopy – localization super-resolution experiments (SMLM: dSTORM, GSDIM, STORM, PALM, PAINT), particle tracking, standard wide-field epifluorescence and TIRF microscopy, transmission microscopy.
- MINFLUX
Functional Imaging and Specialized Technologies
- High-throughput microscopy (HTM)/High content screening (HCS), RNAi screens
- Protein dynamics and interactions (FRET, FCS, FCCS, FLIM, FRAP)
- Multi-photon microscopy
- High resolution episcopic microscopy (HREM)
- Photomanipulation
- High speed imaging
- Feedback microscopy
- Cryo-FM
Mesoscopic Imaging
- Light Sheet mesoscopic imaging: Single-plane illumination microscopy (SPIM), dSLSM
- Optical projection tomography (OPT)
Label-free Imaging
- Quantitative phase imaging (QPI)
- Raman spectroscopy
- Coherent Anti-Stokes Raman Scattering microscopy (CARS)
ISIDORe Services in action
3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations. doi:10.1093/bioinformatics/bty200. Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera
doi: 10.1002/bies.202000257
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003
Virus morphology: Insights from super-resolution fluorescence microscopy
doi: 10.1016/j.csbj.2021.10.038
Sample Characterization
- Atomic force microscopy (AFM)
- MSI - Mass Spectrometry - based Imaging
Electron microscopy for Biological Imaging / Ultrastructural Analysis in 2D & 3D
- Scanning electron microscopy (SEM), including 3D SEM of plastic embedded samples
- Array tomography
- Focused-ion-beam scanning EM (FIB-SEM)
- Serial Block Face Scanning EM (SBF-SEM or SBEM)
- Transmission Electron Microscopy, including Serial section TEM (ssTEM)
- TEM tomography, STEM tomography
- Cryogenic electron Microscopy (Cryo-EM: Cryo-ET, Cryo-SEM, Cryo-FIB, Cryo-TEM)
- Immuno-electron microscopy (immunogold labelling of Tokuyasu cryosections)
ISIDORe Services in action
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003
SARS-CoV-2 infection induces the dedifferentiation of multiciliated cells and impairs mucociliary clearance doi.org/10.1038/s41467-021-24521-x
Correlative Light Microscopy & Electron Microscopy for Biological Imaging
- CLEM from live cells to plastic sections ("live" CLEM)
- Correlative light-electron microscopy from live cells to 3D plastic embedded samples
- Intravital CLEM
- High accuracy on section CLEM
- CLEM on Tokuyasu sections
- CryoCLEM
ISIDORe Services in action
Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies doi.org/10.1038/s42003-020-01567-z
Phase contrast X-Ray Imaging
- Phase contrast X ray imaging (PCI)
ISIDORe Services in action
3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography doi: 10.7554/eLife.60408
Animal imaging (multimodal imaging of small animals)
- Multimodal imaging of small animals
- In vivo optical imaging
- Intravital microscopy
- Magnetic Resonance Imaging (MRI)
- Ultra-sound imaging (US)
- Computed tomography (CT)
- Nuclear imaging (PET, SPECT)
- Bimodal technologies
- Provision of imaging probes/tracers
Animal Monitoring
- Animal behaviour monitoring
- Quantitative spatial-temporal monitoring of individual animals and groups using TrackLab or EthoVision XT software (computer vision, UWB, GPS sensors)
- Computer-aided monitoring: Registration and analysis of manual observations of animals directly or with video feeds/films, potentially including synchronization of data streams, e.g., of physiology by means of The Observer XT
- Animal physiology monitoring
- Body temperature (combined with other variables as required), physiology sensors dependent on the animal species and variables required
Histopathology
- Histopathology
Image Data & Image Analysis
- Biological and Bio-Medical Image data analysis, including consultation and development of novel analysis and visualisation solutions
- AI and Machine Learning (ML)
- Medical Image Data Archiving
ISIDORe Services in action
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003
Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera doi: 10.1002/bies.202000257
Sequencing SERVICES
Provided to you by Emergen & INFRAVEC
Contacts
sequencing-services@isidore-project.eu
The services listed below are available for access regardless of the call for proposals and research topic you select in your pre-application form.
** These services can be provided in combination with or without bioinformatics support.
Genomic sequencing services (BACTERial / viral DNA / RNA genome)
- Illumina technology**
- Oxford Nanopore technology
- Bacterial Genome Sequencing
ISIDORe Services in action
Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075
Metagenome sequencing services
- Shotgun metagenome sequencing (AP-HP CHU Henri Mondor Technologie patent and accreditation): identification of any microorganism (up to 100/week)
- Viral metagenome sequencing: identification of any virus (up to 100/week)
- 16S rRNA metagenome sequencing
- Pan-pathogen surveillance through shotgun metagenomics
ISIDORe Services in action
Identification of necrotizing dermohypodermitis and fasciitis causative microbial agents and microbiota by targeted and shotgun metagenomics
doi: 10.1111/bjd.18611
Inclusion-Body Encephalitis Detected and Characterized by Standardized and Validated Shotgun Metagenomic Approach
doi: 10.3201/eid2609.200366
Fatal Encephalitis Caused by Cristoli virus, a New Emerging Member of the Orthobunyavirus genus of the Peribunyaviridae family
doi: 10.3201/eid2606.191431
Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms
doi: 10.3390/microorganisms8101539
Metagenomic Investigation of Torque Teno Mini Virus-SH in Hematological Patients
doi: 10.3389/fmicb.2019.01898
Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management
doi:10.3390/v10110633
Quality Control Implementation for Universal Characterization of DNA and RNA Viruses in Clinical Respiratory Samples Using Single Metagenomic Next-Generation Sequencing Workflow
doi:10.1186/s12879-018-3446-5
Metatranscriptome sequencing services
- Viral metatranscriptomic – Whole genome sequencing of RNA viruses, including SARS-CoV-2 (up to 100 /week)
ISIDORe Services in action
Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075
Miscellaneous sequencing services
- Small RNA Illumina sequencing**
- Long read DNA sequencing by Nanopore**
- RNAseq total transcriptome Illumina sequencing**
- Genotyping of mosquitoes, insecticide resistance and detection of pathogens
ISIDORe Services in action
Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075
Respiratory pathogens (non-SARS-CoV-2)
Coronaviridae, Orthomyxoviridae, etc.
Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Immunological assays (ELISA, Flow cytometry)
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Lung | |
| Nose | |
| Blood vessel | |
| Liver | |
| Kidney | |
| Brain | |
| 3D tissue and cell printer | |
| Animal | |
| Lung | Pig |
Air Liquid Interface (ALI) polarised cells
| Human | |
| Lung | |
| Airway nasal | |
| Airway tracheal | |
| Airway bronchial | |
| CALU-3 | |
| A549 | |
| Animal | |
| Airway nasal | Sheep |
| Airway tracheal | Sheep, Mouse |
| Airway bronchial | Sheep |
Primary cells
| Human | |
| Immune cells (macrophages, dendritic cells) | |
| Animal | |
| Immune cells (monocytes, macrophages, lymphocytes, dendritic cells) | Cattle, Sheep, Pig |
| Bronchial | Pig |
| Lung | Bat |
| Intestine | Bat |
| Kidney (Avian infectious bronchitis virus model) | Chicken |
| Embryo Kidney (Avian Influenza model) | Chicken |
Tissue section cultures
| Human | |
| Lung precision-cut slices | |
| Placental precision-cut slices | |
| Animal | |
| Lung precision-cut slices | Mouse, Hamster, Pig, Sheep, Cattle, Chicken |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| HTR-8 | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
| DF1 Embryonal fibroblasts | Chicken |
Stem cells
| Human | |
| Mesenchymal | |
| Animal | |
| Mesenchymal | Cattle, Sheep, Pig, Mink, Rabbit |
Engineered cells
| Animal | |
| VERO HSLAM ((Human) signaling lymphocytic activation molecule) | African Green Monkey |
Other
Custom cell requests may be considered.
| Human | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| Animal | |
| Embryonated Specific Pathogen Free Eggs (Avian Influenza model) | Chicken |
| Preparation of tissues | Mammalian and Avian tissues |
Cell model - immortalised cell lines
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Vero E6
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability (incl. high content imaging)
- Bioimaging/Microscopy (incl. high content imaging)
- Flow cytometry
- Immunohistochemistry
- Histological methods
Vero CCL81
- Virus isolation
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR (E, RdRP, N, S)
- Omics - spatial transcriptomics
- Sequencing - NGS
- ELISA (N)
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
- Flow cytometry
- Luminex assay for antibody detection
- Histopathology
- Immunohistochemistry
- Histological methods
Calu 3
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
- Flow cytometry
- Immunohistochemistry
- Histological methods
A549
- Virus titration
- Neutralization assay
- Cytotoxicity
- Antiviral assay
- CPE (TCID50)
- qRT-PCR
- Immunofluorescence
- Cell viability (incl. high content imaging)
- Bioimaging/Microscopy ((conventional - high resolution confocal microscopy ; high content imaging)
Caco-2
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
MDCK
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Hep-2
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Huh-7
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
RPMI-2650
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
human nasal cell line
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Chicken lung epithelial cells
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR - primer sets for chicken innate immune genes)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Pig bronchial epithelial cells
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Cell model - primary cells
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
pig macrophages
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
pig monocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
pig lymphocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
sheep monocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
sheep macrophages (monocyte-derived)
- Virus titration
- Neutralization assay
- Antiviral assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
sheep macrophages (alveolar)
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
sheep macrosheep lymphocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
human primary epithelial lung cells (monolayers/polarised 2D culture)
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
bovine primary epithelial lung cells (monolayers/polarised 2D culture)
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
ovine primary epithelial lung cells (monolayers/polarised 2D culture)
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
cattle macrophages (monocyte-derived)
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
cattle macrophages (alveolar)
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
primary human cell cultures from surgical specimens
- Virus isolation
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Bat lung epithelial cells
- Virus isolation
- Virus titration
- Antiviral assay
- CPE (TCID50)
- qRT-PCR (E, RdRP, N, S)
- Sequencing - NGS
- ELISA (N)
- Immunofluorescence
- Luminex assay for antibody detection
- Histopathology
Bat intestine epithelial cells
- Virus isolation
- Virus titration
- Antiviral assay
- CPE (TCID50)
- qRT-PCR (E, RdRP, N, S)
- Sequencing - NGS
- ELISA (N)
- Immunofluorescence
- Luminex assay for antibody detection
- Histopathology
Swine bronchial epithelial cells
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR )
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Cell model - mesenchymal stem cells
Provided to you by VetBioNet, ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
rabbit mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
mink mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
bovine mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
pig mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
Cell model - Well differentiated and/or polarised cell systems
Provided to you by VetBioNet, ERINHA & EMBRC
Contact
exvivo-invivo-services@isidore-project.eu
ALI-differentiated 2D culture of primary human lung cells
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
ALI-differentiated 2D culture of primary bovine lung cells
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Calu-3 differentiated in ALI conditions
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
A549 differentiated in ALI conditions
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Chicken lung epithelial cells - ALI
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR - primer sets for chicken innate immune genes)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Pig bronchial epithelial cells - ALI
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
RPMI-2650 in ALI 2D cultures
- Vi
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Non-conventional screening models for toxicity and ecotoxicity
Non-conventional screening models for toxicity and ecotoxicity assays:
- zebrafish eggs: up to 48h, 96 well format
- invertebrates (rotifers and artemia): 96 well format
- microalgae
Cell model - Engineered cell lines and primary cells
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Vero hSLAM ((human) signaling lymphocytic activation molecule)
- Virus isolation
- Virus titration
- Neutralization assay
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
- Histopathology
- Immunohistochemistry
- In situ hybridization
Vero E6 with fluorescent viability reporter gene (m-cherry-H2B (histon-2B) protein)
- Cytotoxicity (combined with high-content imaging)
- Cell viability (high-content imaging)
- Bioimaging/Microscopy (high-content imaging)
redifferentiated iPSCs (induced Pluripotent Stem Cells)
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Cell model - Other 2D cell model
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Preparation of mammalian tissues
- Cloning (Cell sorting on plates - 96, 384…)
- Immunofluorescence (conventional and confocal microscopy)
- Bioimaging / microscopy (conventional and confocal microscopy)
- Flow cytometry (multicolor flow cytometry, High Speed cell sorting)
- Histopathology (histology / immunochemistry)
Preparation of avian tissues
- Cloning (Cell sorting on plates - 96, 384…)
- Immunofluorescence (conventional and confocal microscopy)
- Bioimaging / microscopy (conventional and confocal microscopy)
- Flow cytometry (multicolor flow cytometry, High Speed cell sorting)
- Histopathology (histology / immunochemistry)
Swab / saliva collection devices
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Cell model - Organoids
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
human lung organoids
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
bovine lung organoids
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
3D tissue and cell printer
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Cell model - Precision-cut tissue slices cultures
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Bovine lung PCLS (Precision Cut Lung Slices)
- qRT-PCR (Fluidigm medium-throughput qPCR - primer sets for >200 bovine genes, mainly related to immunity)
- ELISA (IL-8; IL-1b,…..)
- Immunofluorescence (confocal microscopy)
- Cell viability (LDH release assay)
Hamster PC lung tissue
- Virus isolation
- Virus titration
- Neutralization assay
- Typing
- Omics - transcriptomic analysis by nanostring assay
- Sequencing - NGS
- Histopathology (incl. Immunohistology)
Sheep primary lung PCLS
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
Cattle primary lung PCLS
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
Mouse primary lung PCLS
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
Cell model - Organotypic culture
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Chicken tracheal culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Chicken lung culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Ferret tracheal culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Ferret lung culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Pig tracheal culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Pig lung culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Cell model - Other 3D cell models
Preparation of little organs for clearing (lung of mouse) with i and u DISCO
- Cloning (Cell sorting on plates - 96, 384…)
- Immunofluorescence (conventional and confocal microscopy)
- Bioimaging / microscopy (conventional and confocal microscopy)
- Flow cytometry (multicolor flow cytometry, High Speed cell sorting)
- Histopathology (histology / immunochemistry)
SERVICES PROVIDED TO YOU BY: VetBioNet, Transvac, Infrafrontier, ERINHA & EMBRC
ISIDORe will only offer access to in vivo models in the absence of adequate alternative methods to achieve an identical result (REPLACE). Please do not forget to check out our wide range of EX VIVO MODELS.
When in vivo models cannot be substituted with any other comparable method, we will use the smallest number necessary for quality science (REDUCE), as well as state-of-the-art practices to protect animal welfare and prevent animal pain and distress (REFINE).
Positively evaluated requests for access to in vivo models will be subjected to institutional ethical evaluation before any implementation can happen.
The services listed below are a general overview of ISIDORe’s in vivo capacities. Models are not available for all species and/or all pathogens. If you want to make sure that we can provide access to your model of interest, please contact us: exvivo-invivo-services@isidore-project.eu
MODELS FOR INFECTION STUDIES
Please note that agents from the Plasmodiidae and Trypanosomatidae famililes can only be studied in Arthropods. Main exceptions are indicated in brackets. Other specific exceptions may apply.
Provided to you by: VetBioNet, Infrafrontier & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse1
- Hamster (available for RG4 pathogens)
- Guinea Pig (not available for vector-borne pathogens)
- Rabbit
- Ferret
- Pig1,3
- Sheep5 (not available for RG4 pathogens)
- Cattle (not available for RG4 pathogens)
- Non-human primates
- Livestock
- Camelids (not available for RG4 pathogens)
- Chicken2 (not available for RG4 pathogens)
- Fruitbats (not available for RG4 pathogens)
- Wildlife2,4 (not available for RG4 pathogens)
- Zebrafish (not available for RG4 pathogens)
- Arthropods (Only available for vector-borne pathogens)
1 Includes models expressing human ACE2
2 Includes avian influenza models
3 Includes pig influenza models
4 Includes vector-transmission models
5 Includes pregnant sheep models
MODELS FOR DRUG EFFICACY STUDIES
Please note that agents from the Plasmodiidae and Trypanosomatidae famililes can only be studied in Arthropods. Main exceptions are indicated in brackets. Other specific exceptions may apply.
Provided to you by: VetBioNet, Infrafrontier & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse1
- Hamster (not available for RG4 pathogens)
- Guinea Pig (not available for vector-borne pathogens)
- Rabbit
- Ferret
- Pig1,3
- Sheep5 (not available for RG4 pathogens)
- Cattle (not available for RG4 pathogens)
- Non-human primates
- Livestock
- Camelids (not available for RG4 pathogens)
- Chicken2 (not available for RG4 pathogens)
- Fruitbats (not available for RG4 pathogens)
- Wildlife2,4 (not available for RG4 pathogens)
- Zebrafish (not available for RG4 pathogens)
- Arthropods (Only available for vector-borne pathogens)
1 Includes models expressing human ACE2
2 Includes avian influenza models
3 Includes pig influenza models
4 Includes vector-transmission models
5 Includes pregnant sheep models
MODELS FOR VACCINE EFFICACY STUDIES
Please note that agents from the Plasmodiidae and Trypanosomatidae famililes can only be studied in Arthropods. Main exceptions are indicated in brackets. Other specific exceptions may apply.
Provided to you by: VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse1
- Hamster (not available for RG4 pathogens)
- Guinea Pig (not available for vector-borne pathogens)
- Rabbit
- Ferret
- Pig1,3
- Sheep5 (not available for RG4 pathogens)
- Cattle (not available for RG4 pathogens)
- Non-human primates
- Livestock
- Camelids (not available for RG4 pathogens)
- Chicken2 (not available for RG4 pathogens)
- Fruitbats (not available for RG4 pathogens)
- Wildlife2,4 (not available for RG4 pathogens)
- Zebrafish (not available for RG4 pathogens)
- Arthropods (Only available for vector-borne pathogens)
1 Includes models expressing human ACE2
2 Includes avian influenza models
3 Includes pig influenza models
4 Includes vector-transmission models
5 Includes pregnant sheep models
MODELS FOR VACCINE IMMUNOGENICITY STUDIES
Provided to you by: VetBioNet, Transvac & EMBRC
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse
- Hamster
- Rabbit
- Ferret
- Pig
- Sheep
- Cattle
- Non-human primates
- Camelids
- Chicken
- Wildlife Zebrafish
MODELS FOR VECTOR RESEARCH
All of the vectors listed below can be provided free of pathogens. Some of the vectors listed below are provided ONLY free of pathogens and are marked with an *. If you want to make sure that we can provide access to your vector of interest, please contact us.
Provided to you by: INFRAVEC
Contact
TNAManager@infravec2.eu
| Aedes spp | (available pathogen-free and carrying members of the Flaviviridae, Togaviridae & Trypanosomatidae1 families) |
| Anopheles spp | (available pathogen-free and carrying members of the Flaviviridae and Plasmodiidae families) |
| Culex spp | (available pathogen-free and carrying members of the Flaviridae family) |
| Culocoides spp* | (avalaible pathogen-free only) |
| Glossina spp* | (avalaible pathogen-free only) |
| Hyalomma spp* | (avalaible pathogen-free only) |
| Lutzomyia spp | (available pathogen-free and carrying members of the Trypanosomatidae1 family) |
| Ornithodoros spp* | (avalaible pathogen-free only) |
| Phlebotomus spp | (available pathogen-free and carrying members of the Trypanosomatidae1 family) |
| Rhipicephalus spp* | (avalaible pathogen-free only) |
| Sergentomyia spp | (available pathogen-free and carrying members of the Trypanosomatidae1 family) |
| Stomoxys spp* | (avalaible pathogen-free only) |
Mosquito mass rearing* (up to 1000, 10 000, 100 000 specimens) may be available under request.
1 including Leishmania
GENERATION OF NEW STUDY MODELS FOR SARS-CoV-2 RESEARCH
Provided to you by: Infrafrontier
Contact
Asrar Ali KHAN
asrar.khan@infrafrontier.eu
- Generation of precision mouse models
- Humanization of mouse model cohorts by AAV-driven hACE2 expression
- Generation of knock-out mice (service starting 2023)
- Generation of knock-in mice (service starting 2023)
DETECTION & CHARACTERIZATION OF IMMUNE TISSUES & CELLS
Provided to you by: EATRIS, VetBioNet, Infrafrontier & ERINHA
Contact
Patricia Carvajal-Vallejos
patriciacarvajal@eatris.eu
- Immune-function profiling
This service is available for access regardless of the call for proposals and research topic that you select in your pre-application form. Antigen-specific T proliferation and cytokine, chemokine and immune factor analysis (mass cytometry, FACSCanto, LSR IV, Symphony, Helios, Bio-Plex Multiplex immunoassay). - Immune-cell profiling
This service is available for access in the following calls for proposals: CALL I (SARS-CoV-2), CALL IV (non-SARS-CoV-2 respiratory pathogens), CALL V (vector-borne pathogens), and CALL VI (Other epidemic-prone pathogens). - Antiviral screening & mucosal immunology
This service is available for access for SARS-CoV-2 research projects. Including human airway models for testing drugs and for virus – cells interaction, to evaluate the role of individual immune subsets in different contexts against infectious disease and to characterize viral isolates. - Detection and quantification of SARS-CoV-2-specific T cells at the single cell level
This service is available for access for SARS-CoV-2 and MPXV research projects - T-cell cloning and expansion
This service is available for access for SARS-CoV-2 research projects. Determination of specificity - Detection and quantification of SARS-CoV-2-specific B cells at the single cell level
This service is available for access for SARS-CoV-2 research projects. - Access to organoids, spheroids & multifluidic devices for immune surveillance (IncuCyte live-cell imaging of spheroids)
This service is available for access for SARS-CoV-2 research projects.- Virus sequencing, non-coding RNA expression and antibody responses to viral antigens with high-content imaging and analysis.
- Access to Multi-site Immuno-analysis of SARS-CoV-2, including analysis of infected samples based on metal tag detection by mass cytometry
DETECTION & CHARACTERIZATION OF THE IMMUNE RESPONSE
Provided to you by: EATRIS, VetBioNet & ERINHA
Contact
Patricia Carvajal-Vallejos
patriciacarvajal@eatris.eu
- Medium‑ to large-scale analysis of immune proteins
The services listed below are available for access for SARS-CoV-2 research projects.- Protein/peptide identification
- Antibody Characterization / Multi-Attribute Method (MAM)
- Post-Translational Modifications Analysis (Glycosylation; Oxidation/Deamination, Glycan Identity)
- High-throughput Quantitative Proteomics – SWATH analysis (untargeted; relative quantification)
- Intact Protein Measurement
- Aggregation and refolding (SEC chromatography)
- Antibody profiling to evaluate the host immune response
- ICS-T-cell-responses (TRM), Virus-immunome profiling
Quantification of cytokines/chemokines (Bio-plex Multiplex Immunoassay), surface and intracellular detection of markers/cytokines (flow cytometry) in infected biological samples - Functional studies of pathogenicity of genetic variants at molecular and cellular level
Including virus sequencing, non-coding RNAs expression and ELISA assay, drugs; drug testing - Epigenetics of immune cells
To study genome-wide epigenetic changes including DNA methylation, histone modifications and non-coding RNAs expression - Immunoprofiling in swine and poultry
Polychromatic flow cytometry assays, single cell immunomics, MHC haplotyping, Luminex cytokine profiling
DETECTION, CHARACTERIZATION & MODULATION OF IMMUNE GENE EXPRESSION
Provided to you by: EATRIS & VetBioNet
Contact
exvivo-invivo-services@isidore-project.eu
The services listed below are available for access regardless of the call for proposals and research topic that you select in your pre-application form.
- siRNA libraries
- Human
- Swine
- Poultry
- sgRNA/CRISPR Cas9 knockout libraries
- Human
- Swine
- Poultry
- Cattle
- RNAseq transcriptomics, 16S NGS microbiome analysis, metabolomics (LC-MS) in livestock
- Swine
- Poultry
- Specific primer sets and protocols for medium-throughput Fluidigm qPCR targeting up to 96 immune genes
- Mice
- Swine
- Cattle
- Chicken
BIO IMAGING FOR IMMUNO PROFILING
Provided to you by: Euro-BioImaging
Contact
info@eurobioimaging.eu
All the services listed below are available for access at BSL-1 or BSL-2 regardless of the call for proposals & topic you select.
- Development and validation of imaging probes
Targeting of specific molecular inflammation markers or subpopulations of immune cells in surrogate infection models in vivo - Biomedical imaging technologies for monitoring the immune system
- PET
- MRI
- CT
- US
- Optical imaging
- Multimodal imaging
- High-throughput Imaging & Bioimage Analysis
PerkinElmer Opera Phenix & Molecular Devices ImageXpress Nano. Automation for sample processing and Imaging in both +37 C and RT. Image analysis pipelines and customized solutions for DNN based segmentation & classification in 2D and 3D.
SUPPORT FOR THE DEVELOPMENT OF DIAGNOSTICS
Provided to you by the Biomedical Research Foundation, Academy of Athens (BRFAA), the Joanneum Research (JR), and Joint Research Center of European Commission (JRC) in collaboration with EU-OPENSCREEN
Due to the high demand in EU-OPENSCREEN services to support Diagnostic and Therapeutic Development, there is insufficient EC funding to provide you with our services at this time. Feel free to submit a pre-application to enter your research proposal into our list of potential future projects. They will be considered in received order, should additional funding become available in the future. Thank you very much for your understanding.
Contact
EU-OPENSCREEN scientific-projects
scientific-projects@eu-openscreen.eu
Charlotte Wit
charlotte.wit@eu-openscreen.eu
All the services listed below are available for access at BSL-1 or BSL-2 regardless of the call for proposals & research topic that you select in your pre-application form:
- Characterization of in-vitro diagnostic devices and sensing platforms
Electron microscopy (SEM-EDX, TEM-EDX); Surface analysis (XPS, TOF-SIMS); Raman Microscope; Array scanner - Assay development (molecular and biochemical) and integration to IVD devices
Customization of existing assays to be integrated into LoCs, biosensors and microfluidics-based devices - Testing of developed and optimized assays, biosensors, LoCs and microfluidics-based devices with well-characterized samples
Extensive biobank of blood & nasopharyngeal samples from patients infected with various viral and bacterial pathogens. - Surface functionalization
Development of surface modification techniques towards biomolecule immobilization and biosensor fabrication or tailoring of surface properties (antifouling, surface energy etc.) - Lab-on-a-Chip molecular diagnostics, multiplexed pathogen detection, variant discrimination
- Lab-on-a-chip design
Simulation-based fluidics design for existing assays - Lab-on-a-chip implementation
Implementation and adaptation of existing assays into foil-based lab-on-chip - Lab-on-a-chip demonstrator
Foil-based lab-on-chip demonstrator device development for existing assays - Matrix customized methods (e.g., non-human samples) and multiplexed pathogen detection
Development/application of rapid, low cost, high throughput molecular methods for population screening
VECTOR MONITORING
Provided to you by INFRAVEC
Contact
TNA Manager
TNAManager@infravec2.eu
Personalized training in the development and application of molecular diagnostics for vector monitoring
Personalized (1-2 people) laboratory training in state-of-the art molecular biology laboratories to develop and apply molecular diagnostics relevant for modern vector monitoring.
Once you have submitted the ISIDORe pre-application below, please complete the Full application for access to this Personalized Training.
Access to the personnal training application
SUPPORT FOR THE DEVELOPMENT OF SMALL MOLECULE THERAPEUTICS
Provided to you by: EU-OPENSCREEN, EU-OPENSCREEN Partners, ERINHA & EMBRC
Due to the high demand in EU-OPENSCREEN services to support Diagnostic and Therapeutic Development, there is insufficient EC funding to provide you with our services at this time. Feel free to submit a pre-application to enter your research proposal into our list of potential future projects. They will be considered in received order, should additional funding become available in the future. Thank you very much for your understanding.
Contacts
EU-OPENSCREEN scientific-projects
scientific-projects@eu-openscreen.eu
Charlotte Wit
charlotte.wit@eu-openscreen.eu
All the services listed below are available for access regardless of the call for proposals & research topic that you select in your pre-application form. The maximum biosafety level of containment for the performance of the experiments is indicated in the description of the services. For confirming the feasibility of your request, please contact us.
Small molecule libraries – provided ONLY in combination with high throughput screening (HTS) services offered below
- Repurposing Library
Preparation of assay-ready plates with drug repurposing libraries containing approved and clinical trial compounds - European Chemical Biology Library (ECBL)
Preparation of assay-ready plates with 100.000 small molecules containing approx. 2464 bioactives - EU-OPENSCREEN Fragment Library
Preparation of plates with approx. 1000 fragments including 88 minifrags - EU-OPENSCREEN Bioactives
Preparation of plates with 2464 bioactives
Assay development, high throughput screening and hit profiling services for identification of active small molecule and host-targeting agents
- Assay development
Assay design and development in a broad range of readouts including phenotypic assays in BSL2-BSL3 facilities (bacterial growth inhibition and viral infection inhibition, cell-based HCS, host cell response), and BSL1 in-vitro target-based assays with specific bacterial, viral and human targets - Biochemical and enzymatic target-based high-throughput screening
High-throughput screening using BSL1 in-vitro target-based assays with specific bacterial, viral and human targets. The assay needs to be HTS-compatible with demonstrated performance in 384-well format. The service includes assay transfer, HTS and hit validation
Do not forget to request library if necessary. - Cell-based high-throughput screening
Cell-based screen including phenotypic, and target-based that can be run in both, human and bacterial, cells in BSL2 facilities. The assay needs to be HTS-compatible with demonstrated performance in 384-well format. The service includes assay transfer, HTS and hit validation
Do not forget to request library if necessary - Low- and medium-throughput screening in BSL3 facilities
Cell-based screen including phenotypic, and target-based that can be run in human cells and pathogen infection models in BSL3 facilities. The service includes assay transfer, screening and hit validation - Fragment screening
Includes assay development, screening and hit validation - Hit validation and profiling
Disease-relevant models, ADMET, ROS‑tox and others
ISIDORe Services in action
The blood-brain barrier is dysregulated in COVId-19 and serves as a CNS entry route for SARS-CoV-2 doi.org/10.1016/j.stemcr.2021.12.011
Characterization of ACE Inhibitors and AT1R Antagonists with Regard to Their Effect on ACE2 Expression and Infection with SARS-CoV-2 Using a Caco-2 Cell Model
doi.org/10.3390/life11080810
X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease
doi: 10.1126/science.abf7945
Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen
doi.org/10.1021/acsptsci.0c00216
A SARS-CoV-2 cytopathicity dataset generated by high-content screening of a large drug repurposing collection
doi.org/10.1038/s41597-021-00848-4
EVALUATION OF THE SELECTIVE ANTIVIRAL ACTIVITY OF AGENTS IN VIRUS-CELL-BASED ASSAYS
Medicinal chemistry support
- Drug design & evaluation in silico
- Hit-to-lead development following HTS of small molecules
- Fragment-to-lead development fragment screening
- Optimization of potency, selectivity and in vitro/in vivo ADMET properties of small molecule drug candidates
- Design and synthesis of target degraders (PROTACs, RIBOTACs)
Natural compound libraries
provided by EMBRC
Contact
Davide Di Cioccio
davide.dicioccio@embrc.eu
- Natural compound libraries (500 compounds) obtained from various marine organisms (bacteria, fungi, sponges)
- >14000 samples (crude extracts and fractions of pre-fractionated extracts) from marine micro-organisms (i.e., fungi, yeast, bacteria, algae) collected during the EU project PharmaSea. Most samples are stored as 10 mg/mL stocks (DMSO), others at different concentrations or solvent (percentage) or as dried stock.
SUPPORT FOR THE DEVELOPMENT OF ANTIBODY THERAPEUTICS
Provided to you by: EU-OPENSCREEN, EU-OPENSCREEN Partners & ERINHA
Due to the high demand in EU-OPENSCREEN services to support Diagnostic and Therapeutic Development, there is insufficient EC funding to provide you with our services at this time. Feel free to submit a pre-application to enter your research proposal into our list of potential future projects. They will be considered in received order, should additional funding become available in the future. Thank you very much for your understanding.
Contacts
EU-OPENSCREEN scientific-projects
scientific-projects@eu-openscreen.eu
Charlotte Wit
charlotte.wit@eu-openscreen.eu
All the services listed below are available for access regardless of the call for proposals & research topic that you select in your pre-application form. Services using replication-competent pathogens are indicated in the descriptions below along with the biosafety level. When applicable, fragments of pathogens are used (e.g., antibody discovery). For confirming the feasibility of your request, please contact us.
Library preparation
- VHH library preparation
Preparation of VHH libraries in phagmid vectors including pSEX81 and pMES4. Libraries from naive or immunized alpaca of very high efficiency.
Nanobody, antibody & antigen identification / engineering
- Nanobody identification
The service covers: - Protein overexpression in E. coli system (vector provided by applicant)
- Protein purification and verification by mass spectrometry
- Phage-display nanobody (VHH) library screen
- Verification of positive clones by ELISA test
- Nanobody sequence identification
- Training
- Antibody discovery and selection from B cells
Identification of antibodies from plasma of convalescent patients by B-cell cloning - Antigen or antibody design and engineering
Design and engineering of antibody with specific functions and suitable formats (IgG, Fab, single chain antibodies); engineering for increased stability, solubility, modulation of complement engagement, multi-specific constructs
Antibody and/or antigen production and characterization
- Antigen and/or antibody production, purification and characterization
Antibody and/or antigen production and purification, quality control of the samples, biophysical characterization (binding affinity, functionality, epitope mapping), in vitro neutralization assays - 3D structural models
3D structural analysis of antibodies, antigens and antibody-antigen complexes with experimentally guided computational simulations - Physico-chemical measurements of quality attributes
Structure, stability, aggregation (digital electrophoresis, DLS, CD, AUC, Multi Detector-AF4, SPR) - Assessment of endotoxin contamination
LAL tests
Evaluation of the selective antiviral activity of antibodies in virus-cell-based assays
3D structural models
3D structural analysis of antibodies, antigens and antibody-antigen complexes with experimentally guided computational simulations
VECTOR RESEARCH: HIGH-THROUGHPUT SCREENING SERVICES
provided to you by INFRAVEC
Contact
TNAManager@infravec2.eu
- Anopheles barcoded screen in vivo
- Standard Membrane Feeding Assay (SMFA) of live mosquitoes
SERVICES PROVIDED TO YOU BY: Transvac, VetBioNet & Instruct
Vaccine development requires a combination of specialized skills and technical capacities not readily available at a single organization. Find all those skills and capacities in our catalogue.
Please note that all in vivo models for studying immunogenicity, adjuvants or vaccine efficacy are available in the IN VIVO MODELS catalogue of services.
The services listed below are available for access regardless of the call for proposals and research topic you select in your pre-application form. When applicable, viral-like particles and/or pseudoviruses are used as study models for pathogens of interest.
VACCINE PLATFORM TECHNOLOGIES: SCREENING, EXPRESSION AND OPTIMISATION - currently not available
Provided to you by: Transvac & VetBioNet
Contacts
Catarina LUIS
Catarina.Luis@euvaccine.eu
William MARTIN
William.Martin@euvaccine.eu
- Cross-platform screening and pre‑clinical optimization with access to vaccine platform technologies (including proteins, viral like particles, viral vectors) and expression systems (including mammalian and insect cells)
Small-to-medium-scale (mg-scale) expression and purification of antigens from multiple candidate constructs. Expression can be compared in multiple expression systems, including P. pastoris, L. lactis, E. coli; Nicotiana; and constitutive/transient expression in mammalian/ insect cells. Vaccine formats include design and production of viral vector vaccines, Adenovirus (human and chimpanzee) and MVA - Custom construction of nanoparticles based on respiratory syncytial virus nucleoprotein as booster for antigen presentation
- Custom construction of recombinant viral proteins in HEK Freestyle cells
- Custom construction of recombinant vaccine
Two available backbones (non-deleted or E1-deleted genomes) derived from the Manhattan vaccine strain of the canine adenovirus type 2 (CAV-2) - Design and development of nanoparticle-based mucosal vaccine systems for SARS-CoV-2 or other respiratory pathogens
- Expression and purification of SARS-CoV structural proteins for vaccination and in vitro diagnostics
Expression systems available: E. coli, baculovirus
VACCINE PROCESS DEVELOPMENT & PRODUCTION - Currently not available
Provided to you by: Transvac*
Contacts
Catarina LUIS
Catarina.Luis@euvaccine.eu
William MARTIN
William.Martin@euvaccine.eu
- Pre‑clinical GLP production services
- Development and implementation of analytical methods for product characterization and process control and monitoring
- GMP manufacturing of starting materials
- GMP manufacturing of clinical materials
*Please note that ISIDORe funding may be limited for high cost GLP and GMP services, but might be provided as paid-for service
VACCINE ADJUVANTS & FORMULATION - currently not available
Provided to you by: Transvac
Contacts
Catarina LUIS
Catarina.Luis@euvaccine.eu
William MARTIN
William.Martin@euvaccine.eu
- Development and characterisation of vaccine formulations with liposomal adjuvants CAF01 and CAF09b
- Provision of CAF01 and CAF09b adjuvants at GMP grade for use in clinical studies
- Development and characterisation of vaccine formulations with adjuvants SWE, SQ, and SMQ and liposome adjuvants LQ and LMQ
- Upscaling of emulsion adjuvants (SQ, SMQ) and liposome adjuvants (LQ, LMQ) from lab-scale to pilot-scale prior to tech-transferto CDMO for GMP production
- Provision of SWE emulsion adjuvant at GMP grade for use in clinical studies
- Formulation and characterisation of vaccine candidates paired with mucosal or parenteral adjuvants.
STRUCTURAL & CHEMICAL CHARACTERIZATION OF VACCINES AND VACCINE ANTIGENS
Provided to you by: Instruct & the Joint Research Centre of the European Commission
Contact
Pauline AUDERGON
pauline@instruct-eric.org
- Structural characterisation of vaccine antigens (bound or unbound) – see also ANALYTICAL SERVICES
- X-ray methods
- From Sample to X-ray diffraction pipelines
- XChem Fragment Screening
- Online crystallography pipeline for Rapid structural characterization of antigens based on CrystalDirect technology
- Bio-SAXS, solution
- NMR technologies, solid state
- Atomic level characterization and/or interactions (IDP, proteins, host's proteins, nucleic acids, etc);
- Quality assurance via NMR (HOS of vaccines, antibodies, antigens/adjuvants);
- Fast fingerprinting/profiling via NMR metabolomics on blood (serum, plasma) and urine
- Fragment-screening by NMR
- Cryo-EM (single particle analysis)
- Scanning electron microscopy (SEM) -Transmission electron microscopy (TEM)
- Cryogenic electron microscopy (Cryo-EM)
- Electron tomography
- Cryo-ET (in combination with EuBi for correlative EM/light microscopy)
- X-ray methods
- Physico-chemical and in-vitro characterization of adjuvant and nanovaccines (such as LNP-mRNA)
Physical attributes (size distribution, particle concentration). Chemical (composition, free/bound cargo; cargo release kinetic); Stability (aggregation, time stability; mRNA/antigen integrity). In vitro toxicity (endotoxin contamination, cytotoxicity, immunotoxicity) - Identification and measurement of key quality attributes of nanovaccines
SERVICES Provided to you by BBMRI
Contact
Łukasz KOZERA
lukasz.kozera@bbmri-eric.eu
The services listed below are available for access only if you select a SARS-CoV-2 research topic
ACCESS TO EXISTING COLLECTIONS OF HUMAN CLINICAL SAMPLES – COVID 19 PATIENTS & CONTROLS
Includes datasets
Download description of available COVID 19 sample collections
Download description of available control sample collections
Download description of other viral infectious disease human sample collections
ON DEMAND COLLECTION OF HUMAN CLINICAL SAMPLES –COVID 19 PATIENTS & CONTROLS
ACCESS TO DATASETS COLLECTED TOGETHER WITH BIOLOGICAL SAMPLES
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ADVICE SERVICES
Provided to you by: EATRIS
Contact
David Morrow
davidmorrow@eatris.eu
You can access these services for all the open calls.
Regulatory oversight & advice
- Assessment of regulatory requirement for marketing authorization
- Scientific advice for preparing an application to the European Medicines Agency
- Informal scientific advice with selected national competent authorities, for highly complex projects
- Pre-clinical and clinical development plan development – Target Product Profile (TPP) and Investigational Medicinal Product Dossier (IMPD)
- Regulatory requirements for trial authorization and subsequent amendments by competent authorities and ethics committees, fast track procedures, coordinated authorization
Support for Clinical Trials
Provided to you by: ECRIN
Contact
Sara RAZA KHAN
sara.raza-khan@ecrin.org
If you are a researcher, principal investigator or Sponsor, reach out to ECRIN for assistance in planning and design of your clinical research proposals. Please note that these services do not encompass the operational costs of conducting a clinical trial.
Protocol Design For Clinical Trials
- Support for clinical trial methodology, selection of trial design, endpoints and core outcome measures
Planning For clinical trials
- Planning of clinical trial operations, including regulatory / ethical requirements, informed consent, data monitoring plan, data management and data sharing plan
- Supporting the development of the main aspects of funding applications including grant proposals and preparation of trial budget
- Support in identifying available funding mechanisms
- Advice on strategies for site selection and patient recruitment
- Task distribution for multinational study management
Open access tools (www.ecrin.org/tools)
ACCESS TO EUROPEAN CLINICAL TRIALS [CLOSED]
Provided to you by: ECRIN
Contact
Sara RAZA KHAN
sara.raza-khan@ecrin.org
Access to ongoing platform trials for new therapeutic, prevention or vaccine intervention arms (Only for SARS-COV-2/COVID-19)
This service offers to conduct clinical trials as new intervention arms in one of the three EU-funded adaptive platform trials (including operational management services such as regulatory/ethical submission of protocol amendments, IMP management, pharmacovigilance, data management, monitoring):
- REMAP‑COVID (also known as REMAP-CAP), an international platform trial for CAP (community acquired pneumonia) initiated in 2014 and rapidly expanded to include COVID-19 patients. Several domains of this trial are exclusive for patients with confirmed or suspected COVID-19.
- EU‑SolidAct a pan-European adaptive platform trial involved with rapid and coordinated investigation of new and repurposed medications to treat Covid-19 in hospitalized patients.
- VACCELERATE (European Corona Vaccine Trial Accelerator Platform), will accelerate phase 2 & 3 COVID-19 vaccine trials.
If you need support for your research on other pathogens with epidemic or pandemic potential such as orthopoxviruses, polio & non polio enteroviruses, or pathogen X, please contact us.
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PROVIDED BY VetBioNet, Transvac, Infrafrontier, ERINHA, EMBRC & Infravec
Find out about and get access to our wide range of in vivo models and expertise for advancing your research on epidemic-prone pathogens
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Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Immunological assays (ELISA, Flow cytometry)
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Lung | |
| Nose | |
| Blood vessel | |
| Liver | |
| Kidney | |
| Brain | |
| 3D tissue and cell printer | |
| Animal | |
| Lung | Cattle |
| Intestinal | Cattle, Chicken |
Air Liquid Interface (ALI) polarised cells
| Human | |
| Lung | |
| Airway nasal | |
| Airway tracheal | |
| Airway bronchial | |
| CALU-3 | |
| A549 | |
| RPMI-2650 | |
| Animal | |
| Lung | Cattle, Chicken, Pig |
| Airway nasal | Sheep, Pig |
| Airway tracheal | Sheep, Pig, Mouse |
| Airway bronchial | Sheep, Pig |
| Intestinal | Cattle, Chicken |
Primary cells
| Human | |
| Immune cells ( macrophages, dendritic cells) | |
| Lung | |
| Cultures from surgical specimens | |
| Animal | |
| Immune cells (monocytes, macrophages, lymphocytes, dendritic cells) | Cattle, Sheep, Pig |
| Lung | Cattle, Sheep, Bat |
| Bronchial | Pig |
| Intestine | Bat |
Tissue section cultures
| Human | |
| Placental precision-cut slices | |
| Animal | |
| Lung Precision Cut slices | Mouse, Hamster, Pig, Sheep, Cattle, |
| Liver Precision Cut slices | Sheep |
Organotypic cultures
| Animal | |
| Lung | Chicken, Ferret, Pig |
| Trachea | Chicken, Ferret, Pig |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| HTR-8 | |
| RPMI-2650 | |
| HEPA-RG | |
| Nasal cell line | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
| Lung | Chicken |
| Bronchial | Pig |
Stem cells
| Human | |
| Mesenchymal | |
| Redifferentiated IPSCS (Induced pluripotent stem cells) | |
| Animal | |
| Mesenchymal | Cattle, Sheep, Pig, Mink, Rabbit |
Engineered cells
| Animal | |
| VERO HSLAM ((Human) signaling lymphocytic activation molecule) | African Green Monkey |
| VERO E6 with fluorescent viability reporter gene (m-Cherry-H2B (Histone-2B) Protein) | African Green Monkey |
Other
Custom cell requests may be considered.
| Human | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| Animal | |
| Preparation of tissues | Mammalian and Avian tissues |
| Preparation of little organs for clearing (Lungs) with I and U DISCO | Mouse |
Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Blood vessel | |
| Liver | |
| Kidney |
Air Liquid Interface (ALI) polarised cells
| Human | |
| A549 |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
Engineered cells
| Human | |
| HUH-7 expressing EBOV VP30 | |
| HUH-7 expressing MARV VP30 | |
| HUH-7 expressing SUDV VP30 | |
| A549 expressing EBOV VP30 | |
| A549 expressing MARV VP30 | |
| A549 expressing SUDV VP30 | |
| Animal | |
| VERO E6 expressing EBOV VP30 | African Green Monkey |
| VERO E6 expressing MARV VP30 | African Green Monkey |
| VERO E6 expressing SUDV VP30 | African Green Monkey |
Other
Custom cell requests may be considered.
| Human | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| Animal | |
| Preparation of tissues | Mammalian and Avian tissues |
All the services listed below are available for access regardless of the call for proposals and research topic that you select in your pre-application form.
SOCIAL SCIENCES SERVICES
Provided to you by: Sonar-Global
Contact
Sarah Marsh ARNAUD
sarah.arnaud@pasteur.fr
Social sciences preparedness and response interventions
- Vulnerability assessments
This service provides ethnographic investigation of locally-defined case definitions of social groups most likely to be marginalized or excluded before or during an epidemic; offer systematic analysis of complex factors leading to or aggravating marginalization - Protocols & implementation for public engagement, acceptability and compliance with epidemic control efforts: clinical trials, nonpharmaceutical interventions, and vaccination
This service will develop protocols for assessing the public engagement, acceptability and compliance with control efforts of targeted measures and if needed, support the implementation of these protocols
Post-intervention evaluation
- Intervention or response evaluation
Evaluation of the planning, development and implementation of specific epidemic intervention or response (including for COVID-19 pandemic) - Ethical evaluation: post-intervention assessment of ethical stakes at country level in West and Central Africa.
Service available for West and Central Africa French-speaking countries.
Evaluation of ethical dimensions/consequences of an intervention, (including and specific to the COVID-19 pandemic): Socio-anthropological assessment based on enquiries with national and local authorities, communities, teams and participants in the project. Offers assessment of social effects of program. Service is available for West and Central Africa French-speaking countries. - Ethical evaluation: Ethical assessment of program/intervention (elsewhere)
Evaluation of ethical dimensions/consequences of an intervention, (including and specific to the COVID-19 pandemic): Ethical evaluation of program or intervention by trained and experienced bioethics team
Scale-up services for qualitative analyses and epidemic response
- Demographic, health, socio-economic data and analyses
Scaling up of existing qualitative analyses to demographic, health and socio-economic data and analyses - Policy analysis
Systematic review of local policy measures and synthesis of key lessons learnt to inform scale-up in preparedness and ongoing response
Cost benefit analysis of epidemic response measure
- Cost benefit analysis of epidemic response measure
Evaluation of costs and benefits associated with public health intervention (including COVID-19), resulting in a report to be delivered at end of service
Community surveillance and social dimensions of outbreak investigation
- Design of community surveillance activities for human and animal health, to complement existing surveillance systems
Develop an adapted, locally appropriate plan for community detection of outbreaks of new COVID-19 waves. This service would enable local public health authorities to identify social risks and to facilitate community engagement and participation in the identification of these risks. Where appropriate, this plan will include human interactions with potential animal reservoirs in which COVID-19 has been detected. Rapid quantitative and qualitative methods, including key informant interviews and targeted focus group discussions will be employed - Design, implementation and supervision of community surveillance activities for human and animal health, to complement existing surveillance systems
Develop an adapted, locally appropriate plan for community detection of outbreaks of new COVID-19 waves. This service would enable local public health authorities to identify social risks and to facilitate community engagement and participation in the identification of these risks. Where appropriate, this plan will include human interactions with potential animal reservoirs in which COVID-19 has been detected. Rapid quantitative and qualitative methods, including key informant interviews and targeted focus group discussions will be employed - Development of protocol of social sciences community investigation of human/animal disease outbreak
This service will offer the development of a protocol to investigate the social dimensions of new outbreaks that may involve spill overs from animals into human beings (as well as spillbacks). The service will provide understanding of specific social, cultural and livelihood dimensions of human-animal interactions as well as concrete recommendations for prevention - Development and implementation of protocol of social sciences community investigation of human/animal disease outbreak
This service will offer the development and implementation of a protocol to investigate the social dimensions of new outbreaks that may involve spill overs from animals into human beings (as well as spillbacks). The service will provide understanding of specific social, cultural and livelihood dimensions of human-animal interactions as well as concrete recommendations for prevention
SERVICES FOR DISEASE VECTOR SURVEILLANCE
Provided to you by: Emergen & INFRAVEC
Contact
sequencing-services@isidore-project.eu
Sequencing services on disease surveillance can be found here.
- Vector field site access and training
- Spacial modelling
FieldWork
Provided to you by: INFRAVEC
Contact
TNAManager@infravec2.eu
Vector fieldwork Services
Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Immunological assays (ELISA, Flow cytometry)
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Lung | |
| Nose | |
| Blood vessel | |
| Liver | |
| Kidney | |
| Brain | |
| Animal | |
| Lung | Cattle, Sheep, Pig |
Air Liquid Interface (ALI) polarised cells
| Human | |
| Lung | |
| Airway nasal | |
| Airway tracheal | |
| Airway bronchial | |
| CALU-3 | |
| A549 | |
| Animal | |
| Lung | Cattle, Chicken |
| Airway nasal | Sheep |
| Airway tracheal | Sheep, Mouse |
| Airway bronchial | Sheep |
Primary cells
| Human | |
| Immune cells ( macrophages, dendritic cells) | |
| Cultures from surgical specimens (Rift valley fever virus model) | |
| Animal | |
| Immune cells (monocytes, macrophages, lymphocytes, dendritic cells) | Cattle, Sheep, Pig |
| Lung | Cattle, Bat |
| Bronchial | Pig |
| Intestine | Bat |
| Hepatocytes | Sheep |
| Maternal epithelial cells | Sheep |
| Umbilical cord derived endothelial cells | Sheep |
| Kidney | Chicken |
Tissue section cultures
| Human | |
| Lung precision-cut slices | |
| Placental precision-cut slices | |
| Animal | |
| Lung precision-cut slices | Mouse, Hamster, Pig, Sheep, Cattle, Chicken |
| Liver precision-cut slices | Sheep |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| HTR-8 | |
| BeWO | |
| HEPA-RG (Rift Valley fever virus model) | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
| Lung | Chicken |
| UMNSAH/DF-1 | Chicken |
| Bronchial | Pig |
| Neuro-2a | Mouse |
| C6/36 | Aedes albopictus |
| Aag2 | Aedes aegypti |
Stem cells
| Human | |
| Mesenchymal | |
| Animal | |
| Mesenchymal | Sheep |
Other
Custom cell requests may be considered.
| Human | |
| Neuronal/Glial cells | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| 3D-vessel-on-a-chip | |
| Animal | |
| Transplacental model (maternal epithelial cells and trophoblasts) | Sheep |
| 3D-vessel-on-a-chip | |
| Preparation of tissues | Mammalian and Avian tissues |
Structural Biology Services
Provided to you by instruct
Contact
Pauline AUDERGON
isidore@instruct-eric.org
The services listed below are available for access regardless of the call for proposals and research topic you select in your pre-application form.
Nanobody discovery
- Generation and characterisation of conformational nanobodies (to facilitate the structural analysis of proteins that are notoriously difficult to purify, to crystallize or to study by another method.)
- Rapid selection of nanobodies by screening/affinity maturation
Crystallography
- Crystallisation of Proteins and Nucleic Acids
- High-throughput Crystallisation
- CrystalDirect Online Crystallography protein-to-structure pipeline
- IceBear crystallography data management (data management, crystallization, data collection)
ISIDORe Services in action:
Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. doi.org/10.1038/s41467-020-17495-9
Protein production for Structural Biology
- Protein expression
- Cloning
- High throughput expression
- Protein purification
- Biomolecular complex purification
Molecular Biophysics
Wide range of techniques to study the biophysical characterization of the structure, function and stability of biological macromolecules like proteins, nucleic acids, lipids and their complexes; as well as the kinetic and thermodynamic parameters of their interaction.
- Circular Dichroism
- Differential Scanning Fluorescence
- Differential Scanning Calorimetry
- Dynamic Light Scattering
- UV/Vis Spectrometry
- Microscale Thermophoresis
- Surface Plasmon Resonance,
- High Throughput Biolayer Interferometry
- Isothermal titration Calorimetry
- Antibody screening in patient sera (Robotein automated Bimolecular analysis platform)
- SEC-MALS (multi-angle light scattering)
ISIDORe Services in action:
Poor antibody response to BioNTech/Pfizer COVID-19 vaccination in SARS-CoV-2 naïve residents of nursing homes. doi:10.1093/cid/ciab998
Single Molecule and Super-Resolution Microscopy for Structural Biology applications (Instruct)
- Single-molecule detection with fluorescence microscopy techniques: using widefield microscopy such as TIRF, super-resolution methods SMLM (STORM, GSD/GSDIM, PALM, PAINT)
Mass Spectrometry
- Native mass spectrometry
- Single cell mass spectrometry
- Proteomic mass spectrometry with possibility for plasma proteome analysis including monitoring of viral and immune response proteins, analysis of single viral proteins and binding to drugs and antibodies
- Glycan analysis by Mass spectrometry
- GC-MS for the analysis of cuticle thickness to test insecticide resistance in mosquitoes
ISIDORe Services in action:
ICAM-1 induced re-arrangements of capsid and genome prime rhinovirus 14 for activation and uncoating. doi.org/10.1073/pnas.2024251118
Electron Microscopy techniques for Structural Biology
- Scanning electron microscopy (SEM)
- Transmission electron microscopy (TEM)
- Cryogenic electron microscopy (Cryo-EM)
- Electron Microscopy Data Processing Services
- Electron tomography
- Cryo-Electron tomography
- Cryo-Correlative Light and EM
ISIDORe Services in action:
Immunization with synthetic SARS-CoV-2 S glycoprotein virus-like particles protects macaques from infection. doi: 10.1016/j.xcrm.2022.100528
In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. doi: 10.1126/science.abd5223
Magnetic Resonance Techniques
- Solution NMR
- Solid state NMR
- Fragment-screening by NMR
- NMR metabolomic
- NMR-based screening of protein-drug interactions
- Glycan analysis by NMR
ISIDORe Services in action:
The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a. doi: 10.1126/sciadv.abm4034
In-Cell NMR Spectroscopy of Functional Riboswitch Aptamers in Eukaryotic Cells. doi:10.1002/anie.202007184
X Ray Structural Biology Techniques
- X-ray crystallography
- Biological small angle scattering (Bio-SAXS),
- X-ray imaging from synchrotron sources
- XChem Fragment Screening
ISIDORe Services in action:
The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a. doi: 10.1126/sciadv.abm4034.
PDB-REDO
Procedure to optimise crystallographic structure models, providing algorithms that make a fully automated decision-making system for refinement, rebuilding and validation.
- PDB-REDO
AlphaFill
AlphaFold models enriched with ligands and co-factors.
- Alphafill
IMAGING SERVICES
Provided to you by Euro-BioImaging ERIC & VetBioNet
Contact
Arina RYBINA info@eurobioimaging.eu
How imaging technologies contribute to understanding viruses
Imaging technologies used to understand COVID-19 infection
Imaging techniques and COVID19 diagnosis
Understanding SARS-CoV-2 replication cycle in human cells
All the services listed below are available for access at BSL-1 or BSL-2 regardless of the call for proposals & research topic that you select in your pre-application form.
Preparation of samples at BSL3 might be accommodated as part of the service.
Imaging services that can be provided directly in BSL-3 containment are marked with an *
Light Microscopy & Advanced Light Microscopy for Biological Imaging
Fluorescence microscopy
- Laser scanning confocal microscopy (LSCM/CLSM)
- Spinning disc confocal microscopy (SDCM)*
- Light sheet microscopy (LSM) and lattice light sheet microscopy (LLSM)
- Structured illumination microscopy (SIM)
- Widefield microscopy: Total internal reflection fluorescence microscopy (TIRF)
- Deconvolution widefield microscopy (DWM)*
- Image scanning microscopy
- Two-Photon Microscopy/Multi-photon microscopy systems
Fluorescence Nanoscopy
- Stimulated Emission Depletion Microscopy (STED)
- Single-molecule localisation microscopy techniques (SMLM): STORM, GSD/GSDIM, PALM
- Reversible optical fluorescence transitions (RESOLFT)
- Super-resolution localization microscopy – localization super-resolution experiments (SMLM: dSTORM, GSDIM, STORM, PALM, PAINT), particle tracking, standard wide-field epifluorescence and TIRF microscopy, transmission microscopy.
- MINFLUX
Functional Imaging and Specialized Technologies
- High-throughput microscopy (HTM)/High content screening (HCS), RNAi screens
- Protein dynamics and interactions (FRET, FCS, FCCS, FLIM, FRAP)
- Multi-photon microscopy
- High resolution episcopic microscopy (HREM)
- Photomanipulation
- High speed imaging
- Feedback microscopy
- Cryo-FM
Mesoscopic Imaging
- Light Sheet mesoscopic imaging: Single-plane illumination microscopy (SPIM), dSLSM
- Optical projection tomography (OPT)
Label-free Imaging
- Quantitative phase imaging (QPI)
- Raman spectroscopy
- Coherent Anti-Stokes Raman Scattering microscopy (CARS)
ISIDORe Services in action
3DClusterViSu: 3D clustering analysis of super-resolution microscopy data by 3D Voronoi tessellations. doi:10.1093/bioinformatics/bty200. Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera
doi: 10.1002/bies.202000257
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003
Virus morphology: Insights from super-resolution fluorescence microscopy
doi: 10.1016/j.csbj.2021.10.038
Sample Characterization
- Atomic force microscopy (AFM)
- MSI - Mass Spectrometry - based Imaging
Electron microscopy for Biological Imaging / Ultrastructural Analysis in 2D & 3D
- Scanning electron microscopy (SEM), including 3D SEM of plastic embedded samples
- Array tomography
- Focused-ion-beam scanning EM (FIB-SEM)
- Serial Block Face Scanning EM (SBF-SEM or SBEM)
- Transmission Electron Microscopy, including Serial section TEM (ssTEM)
- TEM tomography, STEM tomography
- Cryogenic electron Microscopy (Cryo-EM: Cryo-ET, Cryo-SEM, Cryo-FIB, Cryo-TEM)
- Immuno-electron microscopy (immunogold labelling of Tokuyasu cryosections)
ISIDORe Services in action
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003
SARS-CoV-2 infection induces the dedifferentiation of multiciliated cells and impairs mucociliary clearance doi.org/10.1038/s41467-021-24521-x
Correlative Light Microscopy & Electron Microscopy for Biological Imaging
- CLEM from live cells to plastic sections ("live" CLEM)
- Correlative light-electron microscopy from live cells to 3D plastic embedded samples
- Intravital CLEM
- High accuracy on section CLEM
- CLEM on Tokuyasu sections
- CryoCLEM
ISIDORe Services in action
Post-correlation on-lamella cryo-CLEM reveals the membrane architecture of lamellar bodies doi.org/10.1038/s42003-020-01567-z
Phase contrast X-Ray Imaging
- Phase contrast X ray imaging (PCI)
ISIDORe Services in action
3D virtual pathohistology of lung tissue from Covid-19 patients based on phase contrast X-ray tomography doi: 10.7554/eLife.60408
Animal imaging (multimodal imaging of small animals)
- Multimodal imaging of small animals
- In vivo optical imaging
- Intravital microscopy
- Magnetic Resonance Imaging (MRI)
- Ultra-sound imaging (US)
- Computed tomography (CT)
- Nuclear imaging (PET, SPECT)
- Bimodal technologies
- Provision of imaging probes/tracers
Animal Monitoring
- Animal behaviour monitoring
- Quantitative spatial-temporal monitoring of individual animals and groups using TrackLab or EthoVision XT software (computer vision, UWB, GPS sensors)
- Computer-aided monitoring: Registration and analysis of manual observations of animals directly or with video feeds/films, potentially including synchronization of data streams, e.g., of physiology by means of The Observer XT
- Animal physiology monitoring
- Body temperature (combined with other variables as required), physiology sensors dependent on the animal species and variables required
Histopathology
- Histopathology
Image Data & Image Analysis
- Biological and Bio-Medical Image data analysis, including consultation and development of novel analysis and visualisation solutions
- AI and Machine Learning (ML)
- Medical Image Data Archiving
ISIDORe Services in action
Integrative Imaging Reveals SARS-CoV-2-Induced Reshaping of Subcellular Morphologies doi.org/10.1016/j.chom.2020.11.003
Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera doi: 10.1002/bies.202000257
Sequencing SERVICES
Provided to you by Emergen & INFRAVEC
Contacts
sequencing-services@isidore-project.eu
The services listed below are available for access regardless of the call for proposals and research topic you select in your pre-application form.
** These services can be provided in combination with or without bioinformatics support.
Genomic sequencing services (BACTERial / viral DNA / RNA genome)
- Illumina technology**
- Oxford Nanopore technology
- Bacterial Genome Sequencing
ISIDORe Services in action
Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075
Metagenome sequencing services
- Shotgun metagenome sequencing (AP-HP CHU Henri Mondor Technologie patent and accreditation): identification of any microorganism (up to 100/week)
- Viral metagenome sequencing: identification of any virus (up to 100/week)
- 16S rRNA metagenome sequencing
- Pan-pathogen surveillance through shotgun metagenomics
ISIDORe Services in action
Identification of necrotizing dermohypodermitis and fasciitis causative microbial agents and microbiota by targeted and shotgun metagenomics
doi: 10.1111/bjd.18611
Inclusion-Body Encephalitis Detected and Characterized by Standardized and Validated Shotgun Metagenomic Approach
doi: 10.3201/eid2609.200366
Fatal Encephalitis Caused by Cristoli virus, a New Emerging Member of the Orthobunyavirus genus of the Peribunyaviridae family
doi: 10.3201/eid2606.191431
Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses. Microorganisms
doi: 10.3390/microorganisms8101539
Metagenomic Investigation of Torque Teno Mini Virus-SH in Hematological Patients
doi: 10.3389/fmicb.2019.01898
Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management
doi:10.3390/v10110633
Quality Control Implementation for Universal Characterization of DNA and RNA Viruses in Clinical Respiratory Samples Using Single Metagenomic Next-Generation Sequencing Workflow
doi:10.1186/s12879-018-3446-5
Metatranscriptome sequencing services
- Viral metatranscriptomic – Whole genome sequencing of RNA viruses, including SARS-CoV-2 (up to 100 /week)
ISIDORe Services in action
Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075
Miscellaneous sequencing services
- Small RNA Illumina sequencing**
- Long read DNA sequencing by Nanopore**
- RNAseq total transcriptome Illumina sequencing**
- Genotyping of mosquitoes, insecticide resistance and detection of pathogens
ISIDORe Services in action
Evaluation of NGS-Based Approaches for SARS-CoV-2 Whole Genome Characterisation
doi:10.1093/ve/veaa075
Respiratory pathogens (non-SARS-CoV-2)
Coronaviridae, Orthomyxoviridae, etc.
Our cell models are available for the following types of analysis:
- Virus quantification - infectious particles (TCID50, Plaque assay)
- Virus quantification - non-infectious particles (qRT-PCR)
- Neutralization
- Cell viability/cytoxicity
- Immunological assays (ELISA, Flow cytometry)
- Bioimaging (Immunofluorescence, electron microscopy, confocal microscopy, histology, etc.)
To make sure that the type of analysis you are interested in can be performed in specific cell models, please do not hesitate to contact us exvivo-invivo-services@isidore-project.eu
Organoids
| Human | |
| Lung | |
| Nose | |
| Blood vessel | |
| Liver | |
| Kidney | |
| Brain | |
| 3D tissue and cell printer | |
| Animal | |
| Lung | Pig |
Air Liquid Interface (ALI) polarised cells
| Human | |
| Lung | |
| Airway nasal | |
| Airway tracheal | |
| Airway bronchial | |
| CALU-3 | |
| A549 | |
| Animal | |
| Airway nasal | Sheep |
| Airway tracheal | Sheep, Mouse |
| Airway bronchial | Sheep |
Primary cells
| Human | |
| Immune cells (macrophages, dendritic cells) | |
| Animal | |
| Immune cells (monocytes, macrophages, lymphocytes, dendritic cells) | Cattle, Sheep, Pig |
| Bronchial | Pig |
| Lung | Bat |
| Intestine | Bat |
| Kidney (Avian infectious bronchitis virus model) | Chicken |
| Embryo Kidney (Avian Influenza model) | Chicken |
Tissue section cultures
| Human | |
| Lung precision-cut slices | |
| Placental precision-cut slices | |
| Animal | |
| Lung precision-cut slices | Mouse, Hamster, Pig, Sheep, Cattle, Chicken |
Immortalised cell lines
| Human | |
| CALU-3 | |
| A549 | |
| CACO-2 | |
| HEP-2 | |
| HUH-7 | |
| HTR-8 | |
| Animal | |
| VERO E6, VERO CCL81 | African Green Monkey |
| MDCK | Dog |
| DF1 Embryonal fibroblasts | Chicken |
Stem cells
| Human | |
| Mesenchymal | |
| Animal | |
| Mesenchymal | Cattle, Sheep, Pig, Mink, Rabbit |
Engineered cells
| Animal | |
| VERO HSLAM ((Human) signaling lymphocytic activation molecule) | African Green Monkey |
Other
Custom cell requests may be considered.
| Human | |
| Preparation of tissues | |
| Swab/saliva collection devices | |
| Animal | |
| Embryonated Specific Pathogen Free Eggs (Avian Influenza model) | Chicken |
| Preparation of tissues | Mammalian and Avian tissues |
Cell model - immortalised cell lines
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Vero E6
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability (incl. high content imaging)
- Bioimaging/Microscopy (incl. high content imaging)
- Flow cytometry
- Immunohistochemistry
- Histological methods
Vero CCL81
- Virus isolation
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR (E, RdRP, N, S)
- Omics - spatial transcriptomics
- Sequencing - NGS
- ELISA (N)
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
- Flow cytometry
- Luminex assay for antibody detection
- Histopathology
- Immunohistochemistry
- Histological methods
Calu 3
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
- Flow cytometry
- Immunohistochemistry
- Histological methods
A549
- Virus titration
- Neutralization assay
- Cytotoxicity
- Antiviral assay
- CPE (TCID50)
- qRT-PCR
- Immunofluorescence
- Cell viability (incl. high content imaging)
- Bioimaging/Microscopy ((conventional - high resolution confocal microscopy ; high content imaging)
Caco-2
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
MDCK
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Hep-2
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Huh-7
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
RPMI-2650
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
human nasal cell line
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Chicken lung epithelial cells
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR - primer sets for chicken innate immune genes)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Pig bronchial epithelial cells
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Cell model - primary cells
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
pig macrophages
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
pig monocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
pig lymphocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
sheep monocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
sheep macrophages (monocyte-derived)
- Virus titration
- Neutralization assay
- Antiviral assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
sheep macrophages (alveolar)
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
sheep macrosheep lymphocytes
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
human primary epithelial lung cells (monolayers/polarised 2D culture)
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
bovine primary epithelial lung cells (monolayers/polarised 2D culture)
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
ovine primary epithelial lung cells (monolayers/polarised 2D culture)
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
cattle macrophages (monocyte-derived)
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
cattle macrophages (alveolar)
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
primary human cell cultures from surgical specimens
- Virus isolation
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Bat lung epithelial cells
- Virus isolation
- Virus titration
- Antiviral assay
- CPE (TCID50)
- qRT-PCR (E, RdRP, N, S)
- Sequencing - NGS
- ELISA (N)
- Immunofluorescence
- Luminex assay for antibody detection
- Histopathology
Bat intestine epithelial cells
- Virus isolation
- Virus titration
- Antiviral assay
- CPE (TCID50)
- qRT-PCR (E, RdRP, N, S)
- Sequencing - NGS
- ELISA (N)
- Immunofluorescence
- Luminex assay for antibody detection
- Histopathology
Swine bronchial epithelial cells
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR )
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Cell model - mesenchymal stem cells
Provided to you by VetBioNet, ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
rabbit mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
mink mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
bovine mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
pig mesenchymal stem cells
- Neutralization assay
- Antiviral assay
- PRNT/microneutralization
Cell model - Well differentiated and/or polarised cell systems
Provided to you by VetBioNet, ERINHA & EMBRC
Contact
exvivo-invivo-services@isidore-project.eu
ALI-differentiated 2D culture of primary human lung cells
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
ALI-differentiated 2D culture of primary bovine lung cells
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Calu-3 differentiated in ALI conditions
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
A549 differentiated in ALI conditions
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Chicken lung epithelial cells - ALI
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR - primer sets for chicken innate immune genes)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
Pig bronchial epithelial cells - ALI
- Virus titration (Plaque assay titration on MDCK cells)
- Cytotoxicity (CellTiter-Glo assay, automated cell numeration)
- Antiviral assay (ViralTox-Glo assay in microtiter plate format)
- qRT-PCR (Fluidigm medium throughput qPCR)
- Biomaging/microscopy (CellTiter-Glo assay, automated cell numeration)
RPMI-2650 in ALI 2D cultures
- Vi
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
Non-conventional screening models for toxicity and ecotoxicity
Non-conventional screening models for toxicity and ecotoxicity assays:
- zebrafish eggs: up to 48h, 96 well format
- invertebrates (rotifers and artemia): 96 well format
- microalgae
Cell model - Engineered cell lines and primary cells
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Vero hSLAM ((human) signaling lymphocytic activation molecule)
- Virus isolation
- Virus titration
- Neutralization assay
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
- Histopathology
- Immunohistochemistry
- In situ hybridization
Vero E6 with fluorescent viability reporter gene (m-cherry-H2B (histon-2B) protein)
- Cytotoxicity (combined with high-content imaging)
- Cell viability (high-content imaging)
- Bioimaging/Microscopy (high-content imaging)
redifferentiated iPSCs (induced Pluripotent Stem Cells)
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Cell model - Other 2D cell model
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Preparation of mammalian tissues
- Cloning (Cell sorting on plates - 96, 384…)
- Immunofluorescence (conventional and confocal microscopy)
- Bioimaging / microscopy (conventional and confocal microscopy)
- Flow cytometry (multicolor flow cytometry, High Speed cell sorting)
- Histopathology (histology / immunochemistry)
Preparation of avian tissues
- Cloning (Cell sorting on plates - 96, 384…)
- Immunofluorescence (conventional and confocal microscopy)
- Bioimaging / microscopy (conventional and confocal microscopy)
- Flow cytometry (multicolor flow cytometry, High Speed cell sorting)
- Histopathology (histology / immunochemistry)
Swab / saliva collection devices
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Cell model - Organoids
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
human lung organoids
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
bovine lung organoids
- Cytotoxicity
- Antiviral assay
- qRT-PCR
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy (conventional - high resolution confocal microscopy)
3D tissue and cell printer
- Virus titration
- Neutralization assay
- Typing
- Cytotoxicity
- Antiviral assay
- Electron light microscopy
- Focus Forming assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
- Omics - spatial transcriptomics
- Sequencing
- Immunofluorescence
- Cell viability
- Bioimaging/Microscopy
- Flow cytometry
- Immunohistochemistry
- Histological methods
Cell model - Precision-cut tissue slices cultures
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Bovine lung PCLS (Precision Cut Lung Slices)
- qRT-PCR (Fluidigm medium-throughput qPCR - primer sets for >200 bovine genes, mainly related to immunity)
- ELISA (IL-8; IL-1b,…..)
- Immunofluorescence (confocal microscopy)
- Cell viability (LDH release assay)
Hamster PC lung tissue
- Virus isolation
- Virus titration
- Neutralization assay
- Typing
- Omics - transcriptomic analysis by nanostring assay
- Sequencing - NGS
- Histopathology (incl. Immunohistology)
Sheep primary lung PCLS
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
Cattle primary lung PCLS
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
Mouse primary lung PCLS
- Virus titration
- Neutralization assay
- CPE (TCID50)
- PRNT/microneutralization
- qRT-PCR
Cell model - Organotypic culture
Provided to you by VetBioNet & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
Chicken tracheal culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Chicken lung culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Ferret tracheal culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Ferret lung culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Pig tracheal culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Pig lung culture
- Virus isolation
- Virus titration
- CPE (TCID50)
- qRT-PCR
- Sequencing
- ELISA
Cell model - Other 3D cell models
Preparation of little organs for clearing (lung of mouse) with i and u DISCO
- Cloning (Cell sorting on plates - 96, 384…)
- Immunofluorescence (conventional and confocal microscopy)
- Bioimaging / microscopy (conventional and confocal microscopy)
- Flow cytometry (multicolor flow cytometry, High Speed cell sorting)
- Histopathology (histology / immunochemistry)
SERVICES PROVIDED TO YOU BY: VetBioNet, Transvac, Infrafrontier, ERINHA & EMBRC
ISIDORe will only offer access to in vivo models in the absence of adequate alternative methods to achieve an identical result (REPLACE). Please do not forget to check out our wide range of EX VIVO MODELS.
When in vivo models cannot be substituted with any other comparable method, we will use the smallest number necessary for quality science (REDUCE), as well as state-of-the-art practices to protect animal welfare and prevent animal pain and distress (REFINE).
Positively evaluated requests for access to in vivo models will be subjected to institutional ethical evaluation before any implementation can happen.
The services listed below are a general overview of ISIDORe’s in vivo capacities. Models are not available for all species and/or all pathogens. If you want to make sure that we can provide access to your model of interest, please contact us: exvivo-invivo-services@isidore-project.eu
MODELS FOR INFECTION STUDIES
Please note that agents from the Plasmodiidae and Trypanosomatidae famililes can only be studied in Arthropods. Main exceptions are indicated in brackets. Other specific exceptions may apply.
Provided to you by: VetBioNet, Infrafrontier & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse1
- Hamster (available for RG4 pathogens)
- Guinea Pig (not available for vector-borne pathogens)
- Rabbit
- Ferret
- Pig1,3
- Sheep5 (not available for RG4 pathogens)
- Cattle (not available for RG4 pathogens)
- Non-human primates
- Livestock
- Camelids (not available for RG4 pathogens)
- Chicken2 (not available for RG4 pathogens)
- Fruitbats (not available for RG4 pathogens)
- Wildlife2,4 (not available for RG4 pathogens)
- Zebrafish (not available for RG4 pathogens)
- Arthropods (Only available for vector-borne pathogens)
1 Includes models expressing human ACE2
2 Includes avian influenza models
3 Includes pig influenza models
4 Includes vector-transmission models
5 Includes pregnant sheep models
MODELS FOR DRUG EFFICACY STUDIES
Please note that agents from the Plasmodiidae and Trypanosomatidae famililes can only be studied in Arthropods. Main exceptions are indicated in brackets. Other specific exceptions may apply.
Provided to you by: VetBioNet, Infrafrontier & ERINHA
Contact
exvivo-invivo-services@isidore-project.eu
- Mouse1
- Hamster (not available for RG4 pathogens)
- Guinea Pig (not available for vector-borne pathogens)
- Rabbit
- Ferret
- Pig1,3
- Sheep5 (not available for RG4 pathogens)
- Cattle (not available for RG4 pathogens)
- Non-human primates
- Livestock
- Camelids (not available for RG4 pathogens)
- Chicken2 (not available for RG4 pathogens)
- Fruitbats (not available for RG4 pathogens)
- Wildlife2,4 (not available for RG4 pathogens)
- Zebrafish (not available for RG4 pathogens)
- Arthropods (Only available for vector-borne pathogens)
1 Includes models expressing human ACE2
2 Includes avian influenza models
3 Includes