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, direct RNA)
• Epigenomics/Epitranscriptomics: ChIP-seq, RNA m6A methylation
• We have a particular expertise in Nanopore long-read sequencing for transcriptomics, including for single-cell RNA-seq.

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

Equipment

•  Sequencing (short reads): NextSeq 2000 (Illumina)
• Sequencing (long reads): PromethION P2solo, MinION and MinION Mk1C (Oxford Nanopore Technologies)
• Single-cell transcriptomics: Chromium Controller iX (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), and single-cell RNA-seq (Illumina and Nanopore)
• Development of bioinformatics tools:
  • Aozan – an automated post-sequencing data-processing pipeline
    • Article: doi:10.1093/bioinformatics/btx154
    • GitHub: https://github.com/GenomiqueENS/aozan
  • ToulligQC – QC analyses of Oxford Nanopore runs
    • GitHub : https://github.com/GenomiqueENS/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/GenomiqueENS/eoulsan
  • Asarusim – an automated workflow for simulating long-read single-cell Nanopore reads
    • GitHub: https://github.com/GenomiqueENS/AsaruSim

Research and Development

• Single-cell RNA-seq coupled with long-read sequencing

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, Aozan and ToulligQC) 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.
• Sivori M et al, The pelvic organs receive no parasympathetic innervation, eLife (2024) 12:RP91576. https://doi.org/10.7554/eLife.91576.3
• Corre M et al, Alternative splicing induced by bacterial pore-forming toxins sharpens CIRBP-mediated cell response to Listeriainfection, Nucleic Acids Research, Volume 51, Issue 22, 11 December 2023, Pages 12459–12475, https://doi-org.insb.bib.cnrs.fr/10.1093/nar/gkad1033
• Hidalgo M et al, A conserved molecular template underlies color pattern diversity in estrildid finches. Science Advances (2022) Sep 2;8(35):eabm5800. org/10.1126/sciadv.abm5800.
• Orliaguet L. et al. Early macrophage response to obesity encompasses Interferon Regulatory Factor 5 regulated mitochondrial architecture remodelling. Nat Commun (2022) 13, Article number: 5089. org/10.1038/s41467-022-32813-z

Last update July 2024