EXPERIMENT_TITLE: GSM4052980: Hi-C_WT 1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C was performed essentially as previously described (Rao et al., 2014). Briefly, for each template roughly 10 million cells were crosslinked using 2% formaldehyde. In nucleus restriction was performed using MboI. Restriction overhangs were filled in with biotinylated nucleotides followed by blunt-end ligation. A streptavidin pull-down was performed to enrich for ligated sequences. Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Cohesin catalyses the folding of the genome into loops that are anchored by CTCF. The molecular mechanism of how cohesin and CTCF structure the 3D genome has remained unclear. Here we show that a segment within the CTCF N terminus interacts with the SA2-SCC1 subunits of cohesin. A 2.6 Å crystal structure of SA2-SCC1 in complex with CTCF reveals the molecular basis of the interaction. We demonstrate that this interaction is specifically required for CTCF-anchored loops and contributes to the positioning of cohesin at CTCF-binding sites. A similar motif is present in a number of established and novel cohesin ligands, including the cohesin release factor WAPL. Our data suggest that CTCF enables chromatin loop formation by protecting cohesin against loop release. These results provide fundamental insights into the molecular mechanism that enables dynamic regulation of chromatin folding by cohesin and CTCF. Overall design: Hi-C was performed in control and mutant CTCF (Y226A, F228A) HAP1 cells in duplicate.
SAMPLE_TITLE: Hi-C_WT 1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HAP1"}, {"TAG": "cell line", "VALUE": "HAP1"}, {"TAG": "genotype", "VALUE": "Wild-Type"}]
Pool_Member_@attributes_sample_title: Hi-C_WT 1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C_WT 1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_WT_1_L001_R1.fastq.gz", "size": "2690126851", "date": "2019-08-29 15:28:49", "md5": "357dbd331e04b019b8ecb93fb6a2b8e2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC_WT_1_L001_R2.fastq.gz", "size": "2701114429", "date": "2019-08-29 15:27:38", "md5": "4008530dc9bbfb077bdbfc204cb37b65", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR10035372", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10035372/SRR10035372", "size": "2709728398", "date": "2019-08-29 15:30:37", "md5": "e086b87587bd4325e23b689827875e5f", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR10035372.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR010/035/SRR10035372.sralite.1", "size": "1926593574", "date": "2020-06-20 01:33:43", "md5": "6e3720e1721d21aa2549e300367850bf", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]