The ChIP-seq workshop
  • This is a hands-on practical workshop. Each pair of attendees will do a chromatin immuno-precipitation.

    • Crosslink of the material

    • Extraction and fragmentation of the chromatin

    • Immunoprecipitation (of histone post-translational modifications or RNA polymerase)

    • Validation de l'enrichissement par qPCR

  • Sequencing banks will be prepared using partir des IPs with proper enrichment and yields.

  • All the theoretical and practical aspects of the ChIP-seq will be mentioned, from cell crosslink to the bioinformatics analysis

 

  • The practical aspects of the ChIP-seq will be introduced by researchers based in the I2BC.

  • This course will take place in the I2BC

  • Doing a tour of the high-throughput sequencing platform could be considered.

Figure 1: Word cloud obtained using the titles of reasearch articles found on Pubmed using "ChIP-seq" as a keyword

The ChIP-seq results will be analyzed in the "BigData" workshop

  • Bioinformatical and bio-statistical analysis of the results

  • Correlation betweent the epigenome and the transcriptome

ChIP-seq experiment

The ChIP-seq is a molecular biology technique that allows the genome-wide study of DNA/protein interactions. It combines the immunoprecipitation of a protein of interest with the high-throughput sequencing of co-precipitated DNA fragments.

Figure 2: Epigenomics

   Left: Nucleosome (PDB 1aoi)

   Middle: Illumina sequencing slide

   Right: Illumina High-throughput NextSeq 500 sequencer

Figure 3: ChIP-seq for H3K27me3 in drosophila S2 cells. The snapshot is centered on the Bithorax cluster that contains the 3 homeotic genes Ubx, Abd-A, and Abd-B. These genes are repressed in S2 cells and covered by H3K27me3.

Coordinates in Mb along the chr3R (dm6).

Our sponsors :
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Genome

Biology 

Department

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Scientific consultants
  • Claude THERMES, head of the sequenicing platform of th I2BC

  • Robert DEBUCHY, CNRS researcher and in charge of the qPCR training

  • Daan NOORDERMEER, group leader of the "Chromatin Dynamics"

  • Laurent KURAS, group leader of the 'Physiology and Pathogenicity of Stresses'

  • Gaëlle LELANDAIS, Professor in bioinformatics

  • Sébastien BLOYER, Professor in epigenetics

ChIP-seq organizers
  • Benoit MOINDROT

  • Pierre GROGNET

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The ChIP-seq workshop is sponsored and hosted by the Institute for Intergrative Biology of the Cell (I2BC), in the CNRS campus of Gif-sur-Yvette.