The ChIP-seq tracks represent the different profiles of the immunoprecipitations directed at histone modifications found on the Histone 3 N-terminal tails. A total of six histone modifications are used to generate the chromatin profile: H3K4me1, H3K4me3, H3K9me3, H3K27me3, H3K27ac, and H3K36me3. The profile generated can be used with bioinformatic tools (e.g. ChromHMM) to generate genome-wide chromatin profile (1) for a given sample (e.g. tissue, cell population).
The data were generated by the EMC Group at McGill based on a uniform processing pipeline. These datasets were used in all downstream analysis pipelines by members of the EMC Group at McGill.
Samples are crosslinked with formaldehyde, quenched glycine and washed with PBS. The crosslinked samples are then sonicated using the waterbath-based Bioruptor (Diagenode) to create chromatin fragments containing 100-300 bp DNA fragments. The fragmented chromatin samples are then used for immunoprecipitations using the IP-Star (Diagenode) with validated histone antibodies. Theimmunoprecipitated chromatin pulldowns and inputs (without immunoprecipitation) are then reverse crosslinked, RNase treated, proteinase K treated and DNA recovered using silica-based purification columns (Qiagen). The purified samples are then quantified and profiled using the Agilent 2100 BioAnalyzer (Agilent Technologies).
Libraries were prepared according to the Illumina TruSeq DNA protocols with adaptations for low amounts of material; changes includes PCR enrichment prior to size selection instead of after. The libraries get size selected between 200-400 bp using automated electrophoresis gels (SAGE Science). Completed libraries are checked on the Agilent 2100 BioAnalyzer (Agilent Technologies).
Samples were indexed and sequenced in an Illumina HiSeq 2000.
Data were generated and processed in the Epigenomic Mapping Centre (EMC) and Epigenomic Data Coordination Centre (EDCC) of McGill University and the Genome Quebec Innovation Centre (Montreal, QC, Canada). Both EMC and EDCC belong to the Canadian Epigenetics, Environment and Health Research Consortium (CEEHRC) associated with IHEC. Funding was obtained from the Canadian Institutes of Health Research (CIHR) in partnership with Genome British Columbia and Genome Quebec. For inquiries, please contact us at the following address: info (at) epigenomesportal.ca