Genomic analysis

Team:

Margot Jarrige: Platform Manager Engineer (CECS)

Hélène Polvèche: Bioinformatics Engineer (CECS)

plateforme analyse genomique_expression genique

 

 

The NGS platform offers I-Stem research teams high throughput sequencing services for Genome and/or Transcriptome as well as scientific and technical support by proposing sequencing strategies that are best adapted to the projects. At the end of the sequencing, the raw data is analyzed according to the applications and then transferred to the project manager.

The applications available within the platform include:

  • Exome sequencing: analysis of coding regions and identification of mutations (SNP / CNV)
  • Targeted sequencing: analysis of gene panels and identification of mutations (SNP / CNV)
  • Transcriptome sequencing:
    • RNA-seq, quantification of gene expression/transcripts, expression differential between conditions and analysis of splicing variants
    • Coding RNA ( Ampliseq TM, 3′ RNA-seq), quantification of gene expression and expression differential between conditions
    • miRNA-seq, quantification of miRNA expression and expression differential between conditions.

The platform has an Ion Proton sequencer, Ion Chef and Ion OT2/ES (Thermo Fisher Scientific) controllers as well as equipment for sample extraction, quantification and quality control (Qiacube – Qiagen / BioAnalyser – Agilent / QuantStudio 12K & 7K – Thermo Fisher Scientific)

In addition to the service activity, the platform conducts R&D programs such as the development of new sequencing techniques and the implementation of bioinformatics tools (Databases / NGS analysis pipelines)

 

Collaborations:

  • PSMN (Pôle Scientifique de Modélisation Numérique)

 

Publications:

  •  Hoch L, et al (2019). Identification of thiostrepton as a pharmacological approach to rescue misfolded alpha-sarcoglycan mutant proteins from degradation. Scientific Reports
    doi : 10.1038/s41598-019-43399-w
  • Fontrodona N, Aubé F , et al (2019). Interplay between coding and exonic splicing regulatory sequences. Genome Research
    doi : 10.1101/gr.241315.118
  • Maury Y, et al (2018). Human pluripotent stem cell-based drug screening reveals therapeutic potential of repurposable cardiac glycosides in myotonic dystrophy type 1. iScience
    doi : 10.1016/j.isci.2018.12.019
  • Galvan L, et al (2018). The striatal kinase DCLK3 produces neuroprotection against mutant huntingtin. Brain
    doi : 10.1093/brain/awy057
  • Cambon K, et al (2017). Preclinical Evaluation of a Lentiviral Vector for Huntingtin SilencingMol Ther Methods Clin Dev.
    doi : 10.1016/j.omtm.2017.05.001
  • Darvile H, et al (2016). Human Pluripotent Stem Cell-derived Cortical Neurons for High Throughput Medication Screening in Autism: A Proof of Concept Study in SHANK3 Haploinsufficiency Syndrome. EBioMedicine.
    doi : 10.1016/j.ebiom.2016.05.032