EXPERIMENT_TITLE: GSM5526453: 2102Ep_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were crosslinked with 1% formaldehyde for 12 minutes. Chromatin was digested in situ using 2,750 U of DpnII overnight on ~5 million cells permeabilised with 0.3% SDS. After a fill-in reaction containing biotinylated dATP, ends were ligated with 2,000 of T4 DNA ligase. Purified DNA was sonicated to 300-700 bp, and sequencing adaptors ligated using NEBnext Ultra II reagents. To match the HiChIP protocol, DNA was heat denatured, followed by purification, isolation of ligated fragments using streptavidin beads, and library amplification. Libraries were prepared using the NEBNext ultra II DNA library prep kit.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Despite a vast expansion in the availability of epigenomic data, our knowledge of the chromatin landscape at interspersed repeats remains highly limited by difficulties in mapping short-read sequencing data to these regions. In particular, little is known about the locus-specific regulation of evolutionarily young transposable elements (TEs), which have been implicated in genome stability, gene regulation and innate immunity in a variety of developmental and disease contexts. Here we propose an approach for generating locus-specific protein-DNA binding profiles at interspersed repeats, which leverages information on the spatial proximity between repetitive and non-repetitive genomic regions. We demonstrate that the combination of Hi-ChIP and a newly developed mapping tool (PAtChER) yields accurate protein enrichment profiles at individual repetitive loci. Using this approach, we show that young TEs display locus- and tissue-specific chromatin profiles in both mice and humans. Insights gained using our method will be invaluable for dissecting the molecular determinants of TE regulation and their impact on the genome. Overall design: Methylated DNA was immunoprecipitated from Hi-C libraries, and ends were mapped using a pipeline (PAtChER) that uses 3D information to map repetitive reads, producing ChIP-like profiles.
SAMPLE_TITLE: 2102Ep_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "2102Ep"}, {"TAG": "cell line", "VALUE": "2102Ep"}]
Pool_Member_@attributes_sample_title: 2102Ep_HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: 2102Ep_HiC
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