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Connexions
Présentation
Groupes
Group
Group : Milieu Intérieur
Darragh Duffy
Services
Booking siteSingle Cell Biomakers proposes various services to the community :
- Training for autonomous use of the equipment
- Assisted use for a selection of technologies
- Advice and technical support
- Development of new of applications and pipelines
- Scientific collaborations
- Access to different data analysis software and project-tailored bioinformatics support for analysis of large-scale data generated by our technologies
Contact : biomarkers_team@pasteur.fr for more information.
Training @ Teaching
TRAINING The team provides training for the technologies and data-analysis. The trainings are scheduled on a monthly basis. Theoretical and hands-on training sessions are designed for basic and advanced autonomous users. All trainings are […]
Équipements
Booking siteSingle Cell Biomakers is an integrated technology platform for multidimensional cell phenotyping & molecular profiling. We propose single-cell cutting-edge technologies and data analysis pipelines. All technologies are bookable through the PPMS online equipment and training reservation site. The equipment is installed in six dedicated laboratories, with a significant part of the technologies situated within BSL2+ (biosafety level 2 +) environment allowing processing of human and infectious material. View a non-exhaustive list of pathogens currently manipulated in the laboratory.
Laboratories and equipment location
Cell phenotyping and sorting (Flow Cytometry Platform)
- – 3 Conventional cytometers (Symphony A5, LSRFortessa, Cytoflex for simultaneous detection of up to 28 parameters
- – Spectral cytometer (ID7000) for indept phenotyping (>40 parameters) and management of autofluorescence
- – Imaging cytometer MARKII (Luminex): spatial quantification of intra- and inter-cellular processes in cells in suspension
- – 7 Cell sorters (2 Astrios, 4 FACSAria Fusion, 1 FACSAria S6): simultaneous sorting of ≤ 6 cell populations, using ≤28 fluorophores in a single panel. 2 sorters available in Bsl2+ environment for sorting of human and/or infectious material.
- – 2 Magnetic-based cell sorters (AutoMACS): pre-enrichment of rare cell populations.
- – MultiMACS: isolation of targeted cell populations from whole blood.
Cell culture and functional assays in Bsl2+ environment (Biomarkers Platform)
- Fully-equipped cell culture facility
- Hypoxia cabinet XVivo (Biospherix): manipulation and cell culture under controlled O2, CO2, N2, temperature and humidity
- Seahorse (Agilent): measuring cellular glycolysis and mitochondrial respiration under controlled O2, CO2, N2, temperature and humidity
- Incucyte S6 (Sartorius): short- and long-term live-content imaging in any conventional cell culture support
- Amaxa nucleofector (Lonza): nucleofection
Multiplex and ultrasensitive protein quantification (immunoassays) (Biomarkers Platform)
- Bioplex 200 (Biorad) coupled to DropArray (Curiox): quantification of ≤ 200 analytes in cell lysis, supernatants or body-fluids with pM sensitivity from reduced sample (5uL) and reagent volumes.
- Simoa HD-x (Quanterix): digital ELISA for quantification of proteins with fM sensitivity
- SP-X (Quanterix): ultrasensitive multiplex protein detection (10-plex)
- Isolight (Isoplexis): single -cell sectretome analysis (32-plex)
RNA/DNA profiling in bulk (Single Cell Platform)
- Nanostring (Nanostring): direct multiplex RNA quantification (800-plex)
- Bioanalyzer (Agilent): quality control of DNA, RNA, & proteins
- Qubit: RNA-quantification
Multi-modal single cell profiling (Single Cell Platform)
- 10xGenomics (3 instruments): single-cell transcriptomics, single-nuclei transcriptomics CITE-Seq, ATAC-Seq, TCR/BCR rearrangement. Available in Bsl2+ confinement for analysis of human and/or infectious cells.
- Spatial transcriptomics (10xGenomics)
- MARS-Seq
- Biomark (Fluidigm): multiplex single cell real-time PCR (96-plex)
Data analysis
- Schnapps –shiny application for analysis of scRNA-Seq data by biologists
- FLowJo (BD) – a tool of choice for analysis of multidimensional flow cytometry data
- Qlucore- user-friendly PCA tool for analysis of high-dimensional data
BD FACSymphony™ S6 Cell Sorter • BD • FACSymphony S6
The BD FACSymphony™ S6 is a high-performance cell sorter that combines the reliability of the FACSAria Fusion platform with advanced optical capabilities from the FACSymphony A5 Analyzer. This versatile research instrument supports 5 lasers […]
BioPlex 200 – protein quantification • •
BioPlex assays are bead-based assays that can be performed in a mixed array (multiplexed). The reader combines two lasers, fluidics, and real-time digital signal processing to distinguish up to 100 different analytes in the […]
ID7000™ Spectral Cell Analyzer • Sony • ID7000
The Sony ID7000 spectral flow cytometer is a cutting-edge instrument tailored for high-parameter analysis, accommodating 45+ color panels with unmatched precision. Utilizing a 6-laser configuration (320, 355, 405, 488, 561, 637 nm), it offers […]
ImageStreamX – Imaging cytometry • Cytek Biosciences • MarkII
ImageStreamX Mk II The Cytek® Amnis® ImageStream®X Mk II imaging flow cytometer combines the high throughput performance of flow cytometry with the imagery and functional insights of microscopy. This unique combination enables a broad […]
Incucyte – Live cell imaging • Sartorius • Incucyte® SX5 Live-Cell Analysis System
Quantitative live cell imaging in a standard incubator using any traditional culture plate/dish. IncuCyte SX5 supports HD phase-contrast, and 2 fluorescence modules (Green/Red, Green/Orange/NIR) and the FRET based Metabolism Optical Module at 4x, 10x […]
Intelliflex • •
The Luminex xMAP INTELLIFLEX is an advanced multiplexing platform that delivers accurate and reliable protein measurement results. It allows the multiplexing up to 500 analytes in a single sample volume. Designed for a 96- […]
IsoLight • •
The IsoLight is a hub for comprehensive proteomic profiling of each cell type across a large assay menu of single-cell and population chip and software products. With one instrument and companion analysis software, we […]
Meso QuickPlex SQ120 (MSD) • •
MSD technology combines electrochemiluminescence and MULTI‑ARRAY to provide unsurpassed sensitivity and multiplex functionality making it an exceptional detection system. MULTI-ARRAY technology is applied to MULTI-SPOT plates to enable precise quantitation of multiple analytes in […]
2 • nCounter NanoString – Gene expression profiling • •
nCounter FLEX NanoString A digital color-coded barcode technology for direct multiplexed measurement of gene expression. It allows up to 800 mRNA, miRNA or DNA targets to be simultaneously profiled based on molecular “barcodes” and […]
Qubit 2.0 – DNA/RNA quantification • •
Qubit 2.0 Sensitive quantification of DNA, RNA & proteins using fluorescent dyes. Qubit allows distinguishing between DNA, RNA or free nucleotides and the measurement is not affected by the presence of co-purified contaminants.
Seahorse – Cell metabolism • Agilent • Seahorse XFe 96 and XF HS mini
Agilent Seahorse analyzers quantify live-cell metabolism in real time by simultaneously measuring oxygen consumption rate (OCR) and extracellular acidification rate (ECAR). This extracellular flux technology uses integrated optical sensors and a transient microchamber above […]
SP-X • •
Ultra-sensitive Simoa planar array technology. Allows multiplexing up to 10-plex. Benchtop form factor semi-automated offline assay prep.
Symphony S6 – Cell sorter • BD •
5 lasers (355nm, 405nm, 488nm, 561nm, and 637nm) and 29 fluorescent detectors BSL2+ : P2+ pathogens and blood Nozzle sizes : 70um; 85um; 100um; 130um Sorting : 1 to 6 way for tubes and […]
• 10X Genomics • Visium CytAssist
Visium CytAssist is a compact, benchtop instrument that enables the transfer of transcriptomic probes from standard glass slides to Visium slides, for spatial profiling from hematoxylin and eosin (H&E)- or immunofluorescence (IF)-stained tissue sections.
HD-X Analyzer • •
Ultra-sensitive Simoa bead assay technology. Allows the multiplexing up to 6-plex. Floor-standing integrated system. Completely automated assay prep and detection.
MERSCOPE ULTRA • Vizgen • Merscope Ultra
High-resolution in situ spatial genomics platform that offers a tissue-wide view of up to 1000 custom genes at single-cell resolution across 3 cm2 of tissue on a single slide.
• 10X Genomics • Xenium
The Xenium platform delivers high-plex in situ detection for integrated spatial RNA and protein expression at subcellular resolution with nanometer precision.
BioMark – gene expression profiling • •
BioMark Fluidigm The microfluidics-based technology Biomark, is an automated, high-performance PCR system that processes tens to hundreds of samples in parallel at nanoliter volumes for gene expression, genotyping, copy number variation analysis and digital […]
Membres
Milena Hasan
Responsable de Structure
Responsable
Cours
Pasteur Course Advanced immunology
This intensive six-week course, including practical work, lectures, and scientific analysis workshops, covers the fundamental themes of cellular and molecular immunology. For more information and program, please, visit the course webpage.
2025-11-17 09:00:00
2026-01-09 18:00:00
Europe/Paris
Pasteur Course Advanced immunology
This intensive six-week course, including practical work, lectures, and scientific analysis workshops, covers the fundamental themes of cellular and molecular immunology. For more information and program, please, visit the course webpage.
Institut Pasteur, Rue du Docteur Roux, Paris, France
Pasteur Course Single cell gene expression and beyond
The course offers comprehensive theoretical and practical training in all stages of high-throughput single-cell profiling, from sample and library preparation to data analysis. Participants will learn to apply cutting-edge technologies for single-cell multi-omics and […]
2025-06-25 09:00:00
2025-07-02 18:00:00
Europe/Paris
Pasteur Course Single cell gene expression and beyond
The course offers comprehensive theoretical and practical training in all stages of high-throughput single-cell profiling, from sample and library preparation to data analysis. Participants will learn to apply cutting-edge technologies for single-cell multi-omics and […]
Institut Pasteur, Rue du Docteur Roux, Paris, France
Single cell gene expression and beyond
Course Overview The course aims at providing theoretical and hands-on training for all steps of high-throughput single cell profiling, from single-cell sample and library preparation to data analysis, using state-of-the-art technological solutions. Program This […]
2022-06-30 09:00:00
2022-07-06 18:00:00
Europe/Paris
Single cell gene expression and beyond
Course Overview The course aims at providing theoretical and hands-on training for all steps of high-throughput single cell profiling, from single-cell sample and library preparation to data analysis, using state-of-the-art technological solutions. Program This […]
28 Rue du Docteur Roux, Paris, France
10th HKU-Pasteur Immunology Course: December 2-15, 2018
‘Quantitative Immunology’ will be the theme of the 10th anniversary of the HKU-Pasteur Immunology Course. We will explore the ongoing transition from reductionist studies, based on the application of genetic approaches in animal models, […]
2018-12-02 09:00:00
2018-12-15 18:00:00
Europe/Paris
10th HKU-Pasteur Immunology Course: December 2-15, 2018
‘Quantitative Immunology’ will be the theme of the 10th anniversary of the HKU-Pasteur Immunology Course. We will explore the ongoing transition from reductionist studies, based on the application of genetic approaches in animal models, […]
HKU-Pasteur Research Centre, Hong Kong
Projets
Projet Transversal
Outils
Financements
Publications
Télécharger-
2025Human brain cell types shape host-rabies virus transcriptional interactions revealing a preexisting pro-viral astrocyte subpopulation., Cell Rep 2025 Aug; 44(9): 116159.
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2025Immune profiling in subclinical secondary dengue-infected cases reveals adaptive immune signatures correlated to protection from severe dengue., Cell Host Microbe 2025 Jul; 33(7): 1191-1207.e4.
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2025Prolonged Zika Virus NS1 Protein Circulation in Patient Sera Impacts Clinical Outcome Before the Rise of a Specific IgM Response., J Med Virol 2025 May; 97(5): e70368.
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2025Steroid hormone levels vary with sex, aging, lifestyle, and genetics, Science Advances , 2025, 11 (13), pp.eadu6094. ⟨10.1126/sciadv.adu6094⟩.
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2025IL-23 tunes inflammatory functions of human mucosal-associated invariant T cells., iScience 2025 Feb; 28(2): 111898.
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2024Smoking changes adaptive immunity with persistent effects., Nature 2024 Feb; 626(8000): 827-835.
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2024Beyond 40 fluorescent probes for deep phenotyping of blood mononuclear cells, using spectral technology., Front Immunol 2024 ; 15(): 1285215.
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2023Unveiling Candida albicans intestinal carriage in healthy volunteers: the role of micro- and mycobiota, diet, host genetics and immune response., Gut Microbes 2023 Dec; 15(2): 2287618.
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2023Nix interacts with WIPI2 to induce mitophagy., EMBO J 2023 Nov; 42(22): e113491.
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2023Dissecting human population variation in single-cell responses to SARS-CoV-2, Nature, 2023, 53 (8), pp.e2250307. ⟨10.1038/s41586-023-06422-9⟩.
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+Voir la liste complète de publications
Contact
Phone: 01.40.61.30.27
Email: biomarkers_team@pasteur.fr
Address : 25-28 Rue du Docteur Roux
75015 Paris France