EXPERIMENT_TITLE: GSM3110157: siControl_REP1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: In addition to mediating sister chromatid cohesion, cohesin plays a central role in DNA looping and segmentation of the genome into contact domains (TADs). Two variant cohesin complexes that contain either STAG/SA1 or SA2 are present in all cell types. Here we addressed their specific contribution to genome architecture in non-transformed human cells. We found that cohesin-SA1 drives stacking of cohesin rings at CTCF-bound sites and thereby contributes to the stabilization and preservation of TAD boundaries. In contrast, a more dynamic cohesin-SA2 promotes cell type-specific contacts between enhancers and promoters within TADs independently of CTCF. SA2 loss, a condition frequently observed in cancer cells, results in increased intra-TAD interactions, likely altering the expression of key cell identity genes. Overall design: ChIP-seq for cohesin subunits SMC1, SA1 and SA2 was performed in 3 different cell lines (MCF10A, HMEC, HCAEC) and peak calling was done against the input sample from the corresponding cell line. RNA-seq was performed in triplicates in MCF10A cells control depleated from SA1, SA2 or CTCF by means of Dharmacon SMART pool siRNAs. HiC-seq was performed in two replicates in MCF10A cells control and depleated from SA1 and SA2 by means of Dharmacon SMART pool siRNAs. 4C-seq was performed in MCF10A cells control and depleated from SA2 or CTCF.
SAMPLE_TITLE: siControl_REP1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Human Mammary Epithelial Cells"}, {"TAG": "cell type", "VALUE": "MCF10A -Transformed nontumorigenic"}, {"TAG": "experiment", "VALUE": "MCF10A cells were arrested in G1 by means of high confluency culture (150,000 cells per cm2). Hi-C was performed as described (Serra et al., 2017) using MboI enzyme. Two library replicates per condition were sequenced (>200 million reads each)."}]
Pool_Member_@attributes_sample_title: siControl_REP1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: siControl_REP1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ALA_4_read2.fastq.gz", "size": "10482541545", "date": "2020-02-28 08:48:40", "md5": "b3c881d35a6d17fb0b778049bd33e260", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7061198", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7061198/SRR7061198", "size": "14274960635", "date": "2018-04-24 17:54:42", "md5": "0852011ff414bcc6a7ba2c65f0213d4a", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7061198.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR007/061/SRR7061198.sralite.1", "size": "9431451207", "date": "2020-06-23 14:18:09", "md5": "bc550d5c7a4fd24b50a0aa31c1012210", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ALA_4_read1.fastq", "size": "51853979261", "date": "2020-02-28 19:21:39", "md5": "35930dd8a660622e5237b794c41b5ad1", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]