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.

Equipment

• 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)

Bioinformatics

• 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 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).

● Lehmann N, et al.. Eoulsan 2 : an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses. Bioarxiv (2021) doi.org/10.1101/2021.10.13.464219.
● Mazaré N, et al. La traduction locale dans les processus astrocytaires périsynaptiques est spécifique et change après le conditionnement à la peur. Cell Rep (2020) 32(8):108076. doi.org/10.1016/j.celrep.2020.108076.
● Fiorucci AS, et al. Arabidopsis S2Lb lie l’activité AtCOMPASS-like et SDG2 dans H3K4me3 indépendamment de la monoubiquitination de l’histone H2B. Genome Biol (2019) 20(1):100. doi : 10.1186/s13059-019-1705-4.
● Dardalhon-Cuménal D, et al.  Cyclin G et les complexes répressifs Polycomb PRC1 et PR-DUB coopèrent pour la stabilité du développement. PLOS Genetics 2018 14:7 doi.org/10.1371/journal.pgen.1007498.
● Benchouaia M, et al. La transcriptomique comparative met en évidence de nouvelles caractéristiques de la réponse à la privation de fer chez le pathogène humain Candida glabrata. Front Microbiol (2018) 9:2689. doi:10.3389/fmicb.2018.02689.

Last update Nov 2021