EXPERIMENT_TITLE: GSM5942379: shSATB1, 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: shSATB1, Jurkat, Hi-C, Rep 1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Jurkat"}, {"TAG": "cell line", "VALUE": "Jurkat"}, {"TAG": "treatment", "VALUE": "shSATB1"}, {"TAG": "genotype", "VALUE": "SATB1 knockdown"}]
Pool_Member_@attributes_sample_title: shSATB1, Jurkat, Hi-C, Rep 1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: shSATB1, Jurkat, Hi-C, Rep 1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR18284130.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-20/SRR018/18284/SRR18284130/SRR18284130.lite.1", "size": "23855038158", "date": "2022-08-12 13:43:52", "md5": "116764c6333b10754a888fc0c0847265", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR18284130", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR18284130/SRR18284130", "size": "29463399210", "date": "2022-03-25 00:29:19", "md5": "7ba3e2a09c33be68f60e096777f658d4", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "shSATB1_HiC_Rep_1_R2.fastq.gz", "size": "25445064437", "date": "2022-03-25 00:22:50", "md5": "91c35214689ea5f8c63617038df38036", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "shSATB1_HiC_Rep_1_R1.fastq.gz", "size": "25044484275", "date": "2022-03-25 00:25:04", "md5": "9815b1703dca8508a1cb897d2648d72a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]