EXPERIMENT_TITLE: GSM5942377: shCtrl, Jurkat, Hi-C, Rep 1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C experiments was perfomed according to Hi-C 2.0
STUDY_DESCRIPTOR_STUDY_ABSTRACT: SATB1, a nuclear matrix-associated protein, has long been proposed to function as a global chromatin loop organizer in T cells. However, the precise roles of SATB1 in chromatin organization remain elusive. Here we show that the depletion of SATB1 in immortalized T cells led to pronounced changes in gene expression, particularly for genes involved in cell proliferation and T cell activation, as well as 3D genome architecture at multiple scales, including the A/B compartment, topologically associating domains (TADs), and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 led to increased association among the SATB1/CTCF co-occupied sites, as well as increased chromatin contacts across these sites, thereby altering the genome-wide chromatin loop landscape. SATB1 does not regulate genome architecture by modulating CTCF occupancy. Rather, the topological effects imposed by SATB1 may be attributed to SATB1-dependent anchoring of CTCF to the salt extraction-resistant nuclear matrix. Together, our findings suggest that the functional interplay between nuclear matrix and CTCF plays a critical role in orchestrating 3D genome organization. Overall design: We constructed two lentiviral vectors, shCtrl (shRNA control) and shSATB1. After infecting and knocking down the expression of SATB1 in Jurkat cells, we performed Hi-C experiment.
SAMPLE_TITLE: shCtrl, Jurkat, Hi-C, Rep 1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Jurkat"}, {"TAG": "cell line", "VALUE": "Jurkat"}, {"TAG": "treatment", "VALUE": "shCtrl"}, {"TAG": "genotype", "VALUE": "control"}]
Pool_Member_@attributes_sample_title: shCtrl, Jurkat, Hi-C, Rep 1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: shCtrl, Jurkat, Hi-C, Rep 1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR18284132.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR018/18284/SRR18284132/SRR18284132.lite.1", "size": "31836106466", "date": "2022-10-09 01:35:32", "md5": "3a7666ad191aa9ba3e35e8bd8a3348db", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR18284132", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR18284132/SRR18284132", "size": "39577313070", "date": "2022-03-13 06:58:04", "md5": "8c0e5f3421c0eb9524f1635143e84858", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "shCtrl_HiC_Rep_1_R2.fastq.gz", "size": "34551010717", "date": "2022-03-13 06:29:47", "md5": "e1b1f440619e21fd2d65db399d4503b6", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "shCtrl_HiC_Rep_1_R1.fastq.gz", "size": "33311444420", "date": "2022-03-13 06:18:08", "md5": "e225ce855037ba7ae7bc5f828a9d8ee5", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]