EXPERIMENT_TITLE: GSM5942381: shCtrl, Jurkat, Hi-C, All Replicates, Merged; 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, All Replicates, Merged
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, All Replicates, Merged
RUN_SET_RUN_Pool_Member_@attributes_sample_title: shCtrl, Jurkat, Hi-C, All Replicates, Merged
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR18284128.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR018/18284/SRR18284128/SRR18284128.lite.1", "size": "57682803501", "date": "2022-08-04 21:53:09", "md5": "463eef433f7452368c2a785ab17d212f", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR18284128", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR18284128/SRR18284128", "size": "71796556509", "date": "2022-03-25 12:09:39", "md5": "d159a0ffdb3a1aaad59d22728feea45c", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "shCtrl_Jurkat_Hi_C_All_Replicates_Merged_R2.fastq.gz", "size": "62541248393", "date": "2022-03-25 11:56:28", "md5": "8c580703e84ca7e7e19054b5ddfa4c76", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "shCtrl_Jurkat_Hi_C_All_Replicates_Merged_R1.fastq.gz", "size": "60653640074", "date": "2022-03-25 11:52:23", "md5": "ddfed08d2df6044f1091c9025d2e87b8", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]