EXPERIMENT_TITLE: GSM2894552: Hi-ChIP_RAD21_KO; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: See Rowley et al., 2017.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: The faithful inheritance of the epigenome is critical for cells to maintain gene expression programs and cellular identity across cell divisions. We mapped strand-specific DNA methylation after replication forks and show maintenance of the vast majority of the DNA methylome within 20 minutes of replication and inheritance of some hemimethylated CpG dinucleotides (hemiCpGs). Mapping the nascent DNA methylome targeted by each of the three DNA methyltransferases (DNMTs) reveals interactions between DNMTs and substrate daughter cytosines en route to maintenance methylation or hemimethylation. Finally, we show the inheritance of hemiCpGs at short regions flanking CCCTC-binding factor (CTCF)/cohesin binding sites in pluripotent cells. Elimination of hemimethylation causes reduced frequency of chromatin interactions emanating from these sites, suggesting a role for hemimethylation as a stable epigenetic mark regulating CTCF-mediated chromatin interactions. Overall design: Mapping DNA methylation and CTCF/cohesin occupancy on nascent chromatin and DNMT-targeted nascent chromatin
SAMPLE_TITLE: Hi-ChIP_RAD21_KO
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HUES64"}, {"TAG": "cell type", "VALUE": "HUES64 human embryonic stem cells"}, {"TAG": "chip antibody", "VALUE": "RAD21 (abcam, ab992)"}]
Pool_Member_@attributes_sample_title: Hi-ChIP_RAD21_KO
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-ChIP_RAD21_KO
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR6389423.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR006/389/SRR6389423.sralite.1", "size": "2901774204", "date": "2020-06-14 02:07:21", "md5": "a465670ee9a26b45241d321ce62b3094", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR6389423", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR6389423/SRR6389423", "size": "4628979008", "date": "2017-12-19 15:06:30", "md5": "2eedb60e8c317052d1a70447da1db591", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HUES64-3BKO_RAD21_Hi-ChIP_2.fq.gz", "size": "3830501720", "date": "2020-03-08 00:41:41", "md5": "e04d652d2969094822dccb9f1fb32652", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HUES64-3BKO_RAD21_Hi-ChIP_1.fq.gz", "size": "3807025848", "date": "2020-03-08 00:41:41", "md5": "a96f3e0c7919ab02f6fa32358013dbde", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]