High-throughput sequencing

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High-throughput sequencing

The NGS platform provides I-Stem with high throughput genome and/or transcriptome sequencing services as well as scientific and technical support to propose the most suitable sequencing strategies for the projects

DNA sequencing, and more particularly high throughput sequencing, is a technology that allows us to study and better understand the rare genetic diseases on which we work at I-Stem. Depending on the techniques developed, it is possible to search for new mutations responsible for genetic diseases (DNAseq ) or to study the expression of genes in a healthy and/or pathological context (RNAseq – transcriptome study). At the end of the bioinformatics analysis, these data can lead to the identification of new therapeutic targets.

The platform has a NextSeq 550 Illumina sequencer as well as equipment for sample extraction, quantification and quality control (Qiacube – Qiagen / BioAnalyzer – Agilent / QuantStudio 12K & 7K – Thermo Fisher Scientific). Since 2020, the platform also offers single cell sequencing (Single cell RNAseq – Chromium 10X genomics)

In addition to the service activity, the platform conducts R&D programs such as the development of new sequencing techniques or new bioinformatics tools (databases, NGS analysis pipelines, etc.)

Tool developed by the platform:

SIStemA: A large and standardized collection of transcriptome data sets for human pluripotent stem cell research

Our GitHub page :  I-Stem-CECS

Team members

Margot Jarrige

Platform Manager

Margot joined I-Stem in 2014 and gradually specialized in throughput sequencing and gene regulation analysis. Margot holds a Master’s degree in “R&D Biotechnology” from the University of Paris VI and is doing a PhD.

Hélène Polvèche

Bioinformatics Engineer

Hélène arrived in 2015. Integrated in the NGS platform since 2017, she is specialized in “Omics” data as well as in web tools development. Hélène holds a Master’s degree in Structural Biology and Bioinformatics.


PSMN ( Pôle scientifique de modélisation numérique)
ENS de Lyon

The PSMN is a scientific platform of the ENS de Lyon hosting high performance computing resources (HPC). It provides immediate and flexible access to significant computing resources (12,000 cores, end 2019).

Réseau des plateformes de génomiques Paris-Saclay

Academic network of platforms dedicated to genomic analysis, i.e. the study of genomes and transcriptomes, in all types of living organisms. It brings together academic platforms attached to the Life Sciences Department (SDV) of the University of Paris Saclay.


Depletion of WFS1 compromises mitochondrial function in hiPSC-derived neuronal models of Wolfram syndrome.

09 May 2023

Zatyka Malgorzata,

Rosenstock Tatiana R,

Sun Congxin,

Palhegyi Adina M,

Hughes Georgina W,

Lara-Reyna Samuel,

Astuti Dewi,

di Maio Alessandro,

Sciauvaud Axel,

Korsgen Miriam E,

Stanulovic Vesna,

Kocak Gamze,

Rak Malgorzata,

Pourtoy-Brasselet Sandra,

Winter Katherine,

Varga Thiago,

Jarrige Margot,

Polvèche Hélène,

Correia Joao,

Frickel Eva-Maria,

Hoogenkamp Maarten,

Ward Douglas G,

Aubry Laetitia,

Barrett Timothy,

Sarkar Sovan,

Stem cell reports

Generating Functional and Highly Proliferative Melanocytes Derived from Human Pluripotent Stem Cells: A Promising Tool for Biotherapeutic Approaches to Treat Skin Pigmentation Disorders.

29 March 2023

Saidani Manoubia,

Darle Annabelle,

Jarrige Margot,

Polveche Hélène,

El Kassar Lina,

Julié Séverine,

Bessou-Touya Sandrine,

Holic Nathalie,

Lemaitre Gilles,

Martinat Cécile,

Baldeschi Christine,

Allouche Jennifer,

International journal of molecular sciences

SISTEMA: A large and standardized collection of transcriptome data sets for human pluripotent stem cell research.

23 July 2021

Jarrige Margot,

Polvèche Hélène,

Carteron Alexandre,

Janczarski Stéphane,

Peschanski Marc,

Auboeuf Didier,

Martinat Cécile,




Nextseq 550

Nextseq 550

Sequencer of the Illumina range, it allows 30X sequencing of a human genome or 40 transcriptomes in parallel. This equipment offers a flexible throughput allowing the development of a wide range of sequencing applications. (Funded by Genopole and UEVE)

Chromium Controller
10X Genomics

Chromium Controller

It uses microfluidic technology to isolate individual cells in a sample and thus allows the study of gene regulation at the single cell level (UEVE funding)


Hamilton Micro lab Star

Pipetting robot designed to automate the preparation of NGS libraries, guaranteeing better precision and reproducibility for sequencing projects. (Genopole funding)


Qubit 2 Fluorometer

Spectrofluorometer allowing a fast, precise and sensitive quantification of nucleic acids and proteins.


The platform is equipped with a computing server (Ubuntu OS) with 38 cores, 250 GB of RAM and 95 TB of disk space.



It allows the automation of a large number of nucleic acid extraction protocols (DNA, mRNA, tRNA, miRNA …)

Thermofisher scientific

Quantstudio 12k et 7k

These are real-time PCR instruments for studying the expression of genes of interest in 96- or 384-well format. Compatible with SYBER and TaqMan chemistry, the Quantstudio offers a wide range of genomic applications. (Genopole funding)


Bioanalyzer 2100

This equipment uses micro-fluidic technology for the analysis of nucleic acid or protein samples. The unique resolution of this device allows quality control of biological samples as well as the identification of small genomic insertions or deletions.

Beckmann et coulter

Ultracentrifugeuse Optima-XE

This device is used to centrifuge biological samples at very high speed to isolate certain particles (UEVE funding)

Malvern Panalytical

NanoSight NS300

It allows the visualization, qualification and quantification in real time of nanoparticles present in a biological fluid (UEVE funding)