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.

Justine Rousselot

Platform Technician (CECS)

After a DUT in Biological Engineering and an initial specialization in robotics and NGS, Justine joined I-Stem in February 2024, as a platform technician. She will be working in both the High-Throughput Screening (HTS) and High-Throughput Sequencing (NGS) teams.

Collaborations

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).

GENOPS
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.

Publications

Synergism of dual AAV gene therapy and rapamycin rescues GSDIII phenotype in muscle and liver.

16 May 2024

Jauze Louisa,

Vie Mallaury,

Miagoux Quentin,

Rossiaud Lucille,

Vidal Patrice,

Montalvo-Romeral Valle,

Saliba Hanadi,

Jarrige Margot,

Polveche Helene,

Nozi Justine,

Le Brun Pierre-Romain,

Bocchialini Luca,

Francois Amandine,

Cosette Jeremie,

Rouillon Jérémy,

Collaud Fanny,

Bordier Fanny,

Bertil-Froidevaux Emilie,

Georger Christophe,

Van Wittenberghe Laetitia,

Miranda Adeline,

Daniele Nathalie,

Gross David,

Hoch Lucile,

Nissan Xavier,

Ronzitti Giuseppe,

JCI insight

The AMPK-related kinase NUAK1 controls cortical axons branching by locally modulating mitochondrial metabolic functions.

21 March 2024

Lanfranchi Marine,

Yandiev Sozerko,

Meyer-Dilhet Géraldine,

Ellouze Salma,

Kerkhofs Martijn,

Dos Reis Raphael,

Garcia Audrey,

Blondet Camille,

Amar Alizée,

Kneppers Anita,

Polvèche Hélène,

Plassard Damien,

Foretz Marc,

Viollet Benoit,

Sakamoto Kei,

Mounier Rémi,

Bourgeois Cyril F,

Raineteau Olivier,

Goillot Evelyne,

Courchet Julien,

Nature communications

Mono- and Biallelic Inactivation of Huntingtin Gene in Patient-Specific Induced Pluripotent Stem Cells Reveal HTT Roles in Striatal Development and Neuronal Functions.

01 January 2024

Louessard Morgane,

Cailleret Michel,

Jarrige Margot,

Bigarreau Julie,

Lenoir Sophie,

Dufour Noëlle,

Rey Maria,

Saudou Frédéric,

Deglon Nicole,

Perrier Anselme L,

Journal of Huntington's disease

SEE ALL THE PUBLICATIONS

Equipments

Nextseq 550
Illumina

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

Hamilton Micro lab Star

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

Thermofisher

Qubit 2 Fluorometer

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

Serveur

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

Qiagen

Qiacube

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)

Agilent

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)