Expertise

The facility supports its collaborators by providing access to high-throughput sequencing, with particular expertise in functional genomics applications in eukaryotes :

• Transcriptomics: RNA-seq (low input, long-read, single-cell)
• Epigenomics/Epitranscriptomics: ChIP-seq, RNA m6A methylation

We also propose a sequencing service “ready-to-load” for users who make their own libraries.

Equipments

• Sequencing (short reads): NextSeq 2000 and NextSeq 500 (Illumina)
• Sequencing (long reads): MinION and MinION Mk1C (Oxford Nanopore Technologies)
• Single-cell transcriptomics: Chromium Controller (10x genomics)

Main achievements

Our platform hosts medium-sized projects (around ten samples per project) on a varied number of model or non-model eukaryotic species (more than twenty currently ranging from fungi to mammals) with topics mainly related to development, neuroscience and genetic regulation. The projects we take on are very often limited in terms of the quantity of starting material and we have now developed a real expertise in the management of this type of studies.

We also have a bioinformatics tool development activity focused on the analysis and automated quality control of the projects we process. We have developed innovative solutions (Eoulsan and Aozan) using calculation distribution tools (cloud computing, MapReduce, Hadoop), traceability and source code availability (GitHub and Docker).

Bioinformatics analysis

For collaborative projects sequenced in our facility we perform quality controls, RNA-seq differential analyses (including complex designs) on Illumina and Nanopore datasets, isoform identification (Nanopore), m6A methylation detection for direct RNA sequencing (Nanopore) and scRNA-seq using Cell Ranger

• Development of bioinformatics tools:
  • Aozan – an automated post-sequencing data-processing pipeline
    • Article: doi:10.1093/bioinformatics/btx154
    • GitHub: https://github.com/GenomicParisCentre/aozan
  • ToulligQC – QC analyses of Oxford Nanopore runs
    • GitHub : https://github.com/GenomicParisCentre/toulligQC/
  • Eoulsan – an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses
    • Original Article: doi:10.1093/bioinformatics/bts165
    • Update preprint: doi.org/10.1101/2021.10.13.464219
    • GitHub: https://github.com/GenomicParisCentre/eoulsan

Research and Development

• Single-cell RNA-seq coupled with long-read sequencing;
• Single-cell RNA-seq on fixed cells (ACME protocol).

Main achievements

Our facility hosts medium-sized projects on more than 20  model or non-model eukaryotic species, with topics mainly related to development, neuroscience and genetic regulation. The projects we collaborate on are often limited in terms of amount of starting material (low input), thanks to which we have developed a real expertise in the management of this type of experimental designs.

Our facility has a recognized expertise in Nanopore long-read transcriptomics, and we have organised six training sessions in 2021 to teach how to use a MinION sequencer (wet-lab and bioinformatics).

We also have a bioinformatics tool development activity focused on the analysis, traceability and automated quality control of data. We have developed innovative solutions (Eoulsan, Aozan and ToulliqQC), maintained over time, and freely available to the community (code available on GitHub with Docker images).

• Lehmann N, Perrin S, Wallon C, Bauquet X, Deshaies V, Firmo C, Du R, Berthelier C, Hernandez C, Michaud C, Thieffry D, Le Crom S, Thomas-Chollier M, Jourdren L. Eoulsan 2: an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyse Bioarxiv 2021 doi.org/10.1101/2021.10.13.464219
• Mazaré N, Oudart M, Moulard J, Cheung G, Tortuyaux R, Mailly P, Mazaud D, Bemelmans AP, Boulay AC, Blugeon C, Jourdren L, Le Crom S, Rouach N, Cohen‑Salmon M. Local Translation in Perisynaptic Astrocytic Processes Is Specific and Changes after Fear Conditioning. Cell Rep 2020 Aug 25;32(8):108076. org/10.1016/j.celrep.2020.108076
• Fiorucci AS, Bourbousse C, Concia L, Rougée M, Deton-Cabanillas AF, Zabulon G, Layat E, Latrasse D, Kim SK, Chaumont N, Lombard B, Stroebel D, Lemoine S, Mohammad A, Blugeon C, Loew D, Bailly C, Bowler C, Benhamed M, Barneche F Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination. Genome Biol 2019 May 21;20(1):100. doi: 10.1186/s13059-019-1705-4.
• Dardalhon-Cuménal D, Deraze J, Dupont CA, Ribeiro V, Coléno-Costes A, Pouch J, Le Crom S, Thomassin H, Debat V, Randsholt NB, Peronnet F. Cyclin G and the Polycomb Repressive Complexes PRC1 and PR-DUB cooperate for developmental stability. PLOS Genetics 2018 14:7 org/10.1371/journal.pgen.1007498
• Benchouaia M, Ripoche H, Sissoko M, Thiébaut A, Merhej J, Delaveau T, Fasseu L, Benaissa S, Lorieux G, Jourdren L, Le Crom S, Lelandais G, Corel E, Devaux F Comparative Transcriptomics Highlights New Features of the Iron Starvation Response in the Human Pathogen Candida glabrata. Front Microbiol 2018 Nov 16;9:2689. doi:10.3389/fmicb.2018.02689.

Last update Nov 2021