EXPERIMENT_TITLE: GSM3489136: C029: Jurkat Hi-C; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Nuclear DNA was extracted after 1 million Jurkat T cells were crosslinked with 1 % formaldehyde for 10 min at room temperature with gentle rotation and permeabilized with freshly prepared ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% Igepal CA630 and 1x Roche complete protease inhibitors). Nuclear DNA was digested by MboI; the ends of the digested fragments were filled in with biotin-14-dATP. The crosslinks were reversed after overnight proximity ligation of the crosslinked DNA fragments. Ligated DNA was purified and sheared to a length of 400 bp; ligation junctions were pulled down with streptavidin C1 beads. Pulled down DNA-on-beads was amplified by PCR with NEBNext Universal primers and index primers. PCR products (library) were cleaned up by 1.0x Agencourt AMPure XP beads. The purified library was run as a smear on 1.5% agarose gel and validated with ClaI digestion.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We performed Hi-C on untreated Jurkat T cells growing in culture. We obtained contact maps with a final resolution of 5 kb where Topologically Associated Domains (TADs) are clearly visible. We identified 3D sub-compartments, characterized by enriched Hi-C contacts within themselves compared to contacts with other compartments. Our results suggest that the A compartment, associated with ongoing transcription, consists of two distinct sub-compartments called A1 and A2; and that the B compartment, associated with lack of transcription, consists of three sub-compartments called B1, B2 and B3. Genes in the A1 and A2 compartments are typically expressed at the same level, but chromatin marks associated with transcription, such as H3K4me2 or H3K27ac, are typically more abundant in A1 than in A2. The B1, B2 and B3 sub-compartments correspond to Polycomb, HP1 and lamina-associated chromatin, which were previously identified types of silent chromatin. Overall, these results suggest that spatial neighborhoods of the Jurkat nucleus correspond to homogeneous chromatin types, and that transcriptionally active regions are in fact two distinct types. Overall design: Two Hi-C libraries were prepared from independent Jurkat T cell cultures.
SAMPLE_TITLE: C029: Jurkat Hi-C
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Immortalized human T lymphocyte Jurkat cell line"}, {"TAG": "cell line", "VALUE": "Jurkat"}, {"TAG": "cell type", "VALUE": "T lymphocyte"}, {"TAG": "start number of the cells", "VALUE": "1 million cells"}]
Pool_Member_@attributes_sample_title: C029: Jurkat Hi-C
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR8244644", "SUBMITTER_ID": "GSM3489136_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS4078629", "EXTERNAL_ID": ["SAMN10477676", "GSM3489136"]}, "@attributes": {"member_name": "", "accession": "SRS4078629", "sample_name": "GSM3489136", "sample_title": "C029: Jurkat Hi-C", "spots": "21563070", "bases": "3234460500", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR8244644.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR008/244/SRR8244644/SRR8244644.sralite.1", "size": "811641567", "date": "2020-06-14 09:49:29", "md5": "59a5beecbf2f800c7d885fa019b26940", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR8244644", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8244644/SRR8244644", "size": "1279028995", "date": "2018-11-26 15:31:13", "md5": "60c54d59372f3ffee53bc269ac266291", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "C029_1_jurkat_wt_read2.fastq.gz", "size": "1004200624", "date": "2020-03-12 04:24:47", "md5": "12d0bb5b0a87ea5e3569eca5d9cf7ec8", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "C029_1_jurkat_wt_read1.fastq.gz", "size": "941568527", "date": "2020-03-12 04:24:47", "md5": "dfb7e8fe9bc4dd446df6eeb0418e0621", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "21563070"}}, "Databases": {"Database": {"Table": {"Statistics": {"Rows": null, "Elements": null, "@attributes": {"source": "meta"}}, "@attributes": {"name": "SEQUENCE"}}}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "3234460500"}}, "@attributes": {"alias": "GSM3489136_r1", "accession": "SRR8244644", "total_spots": "21563070", "total_bases": "3234460500", "size": "1279027462", "load_done": "true", "published": "2018-11-29 16:06:04", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR8244645", "SUBMITTER_ID": "GSM3489136_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS4078629", "EXTERNAL_ID": ["SAMN10477676", "GSM3489136"]}, "@attributes": {"member_name": "", "accession": "SRS4078629", "sample_name": "GSM3489136", "sample_title": "C029: Jurkat Hi-C", "spots": "309132477", "bases": "46369871550", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "C029_2_jurkat_wt_read1.fastq.gz", "size": "16668674886", "date": "2020-03-12 04:24:47", "md5": "0a9048490cb0a7be044c068e730fded4", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR8244645.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-11/SRR008/244/SRR8244645/SRR8244645.sralite.1", "size": "12084412135", "date": "2021-06-15 13:29:30", "md5": "9f7a649329f959cc39ea2a9c95d8ab63", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR8244645", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR8244645/SRR8244645", "size": "21279409503", "date": "2018-11-26 17:29:24", "md5": "2a08672e28c5e2d4faf7c1567e7dcc6e", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "C029_2_jurkat_wt_read2.fastq.gz", "size": "17051606497", "date": "2020-03-12 02:17:08", "md5": "4598043d629d58b10f9fa4854ab5a251", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "309132477"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "46369871550"}}, "@attributes": {"alias": "GSM3489136_r2", "accession": "SRR8244645", "total_spots": "309132477", "total_bases": "46369871550", "size": "21279407755", "load_done": "true", "published": "2018-11-29 16:06:04", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]