The ChIP-seq workshop
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This is a hands-on practical workshop. Each pair of attendees will do a chromatin immuno-precipitation.
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Crosslink of the material
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Extraction and fragmentation of the chromatin
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Immunoprecipitation (of histone post-translational modifications or RNA polymerase)
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Validation de l'enrichissement par qPCR
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Sequencing banks will be prepared using partir des IPs with proper enrichment and yields.
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All the theoretical and practical aspects of the ChIP-seq will be mentioned, from cell crosslink to the bioinformatics analysis
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The practical aspects of the ChIP-seq will be introduced by researchers based in the I2BC.
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This course will take place in the I2BC
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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
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Bioinformatical and bio-statistical analysis of the results
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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).
After having carried out the ChIP experiments at I2BC, the students spend a day with our partner Illumina and start sequencing their libraries.
Our sponsors :
Genome
Biology
Department
Sequencing at the Illumina Solution Center Paris
ChIP-seq organizers
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Benoit MOINDROT
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Pierre GROGNET
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.