EXPERIMENT_TITLE: GSM2395407: HeLa Nucleolus Hi-C rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Nucleoli isolation. Resuspend 2 – 5 x 106 cells with 1.5 ml 0.5% sodium dodecyl sulfate (SDS) and incubate at 62℃ for 5-10 min in order to dissolve the cell membrane. Then add 1.5 ml buffer S1 (0.25 M sucrose and 10 mM MgC12), mix well, and break the cells with ultra-sonication. Monitor the cells under a microscope and stop when over 80% of the cells are burst, leaving intact nucleolus with cytoplasmic materials. Transfer the liquid to a 15 ml tube, carefully add 3 ml buffer S2 (0.35M sucrose, 0.5mM MgC12) to the bottom of the tube and keep the two layers cleanly separated. Centrifuge at 3000 rpm for 5 min at 4℃ and discard the supernatant. Resuspend the pellet with 3 ml buffer S2, filtered with 5 um filter (Millipore) and transferred to a new 15 ml tube. Carefully add 3 ml buffer S3(0.88M Sucrose, 0.5mM MgC12) to the bottom of the tube and keep the two layers cleanly separated. Centrifuge at 4000 rpm for 10 min at 4℃ and discard the supernatant. Resuspend with 100 ul buffer S3, check pure isolated nucleoli under a microscope and store at -80℃. All libraries were prepared for sequencing using standard Illumina protocols
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Nucleolus plays a key role in organizing global nuclear structure and facilitating gene regulation, but the three dimensional information within the nucleolus associated chromatins are still unknown, so here we development the Nucleolus Hi-C (NHi-C) experimental technique, which combines the nucleolus isolation with Hi-C experiment, and study the interactions within and surrounding nucleolus in human cells with a high resolution. With NHi-C experiment, we report how the nucleolus-associated chromatin regions interact at genome scale, and how these interactions organize the repressive nucleus architecture. Overall design: in situ  Hi-C and Nucleolus Hi-C data in human cells to detect the 3D genome information, the detailed information about all files uploaded to GEO for this study are explained in "DataFiles.README"
SAMPLE_TITLE: HeLa Nucleolus Hi-C rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HeLa Nucleolus Hi-C biological repeat 1"}, {"TAG": "cell line", "VALUE": "HeLa"}, {"TAG": "cell type", "VALUE": "cervical cancer"}]
Pool_Member_@attributes_sample_title: HeLa Nucleolus Hi-C rep1
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR5031955", "SUBMITTER_ID": "GSM2395407_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS1805844", "EXTERNAL_ID": ["SAMN06033663", "GSM2395407"]}, "@attributes": {"member_name": "", "accession": "SRS1805844", "sample_name": "GSM2395407", "sample_title": "HeLa Nucleolus Hi-C rep1", "spots": "56625538", "bases": "16987661400", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hela-n-hic-rep1_DO15081210_HF3V3CCXX_L3_2.fq.gz", "size": "5611561923", "date": "2021-02-01 20:39:36", "md5": "9c8db106ccb3c2f2ac9f717dbdb73e40", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5031955", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5031955/SRR5031955", "size": "8069752641", "date": "2016-11-17 18:04:11", "md5": "9c84389dd64fff1c7bd2f3278f499b81", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5031955.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR005/031/SRR5031955.sralite.1", "size": "4250555629", "date": "2021-06-15 04:30:44", "md5": "218929873ac1226711147fd49975382f", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hela-n-hic-rep1_DO15081210_HF3V3CCXX_L3_1.fq.gz", "size": "5134871440", "date": "2021-02-01 20:00:01", "md5": "3f8f6895ce48d445b91c68da7f56ab28", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "56625538"}}, "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": "16987661400"}}, "@attributes": {"alias": "GSM2395407_r1", "accession": "SRR5031955", "total_spots": "56625538", "total_bases": "16987661400", "size": "8069751416", "load_done": "true", "published": "2017-11-22 17:47:24", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR5031956", "SUBMITTER_ID": "GSM2395407_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS1805844", "EXTERNAL_ID": ["SAMN06033663", "GSM2395407"]}, "@attributes": {"member_name": "", "accession": "SRS1805844", "sample_name": "GSM2395407", "sample_title": "HeLa Nucleolus Hi-C rep1", "spots": "56825005", "bases": "17047501500", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5031956", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5031956/SRR5031956", "size": "8157235204", "date": "2016-11-17 17:43:13", "md5": "8fef225989fe74c3edaf6cdeb5f0d9dd", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5031956.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR005/031/SRR5031956.sralite.1", "size": "4264217420", "date": "2021-06-16 07:05:25", "md5": "debc2fd7aa837dcbd031a9fb8c810ea0", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hela-n-hic-rep1_DO15081210_HF3V3CCXX_L4_2.fq.gz", "size": "5657101472", "date": "2021-02-01 20:24:50", "md5": "09a9cfc8434f756dc645286f0086394a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hela-n-hic-rep1_DO15081210_HF3V3CCXX_L4_1.fq.gz", "size": "5196885837", "date": "2021-02-01 20:23:15", "md5": "cbda550f0ba25949c2608ba1fb1be168", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "56825005"}}, "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": "17047501500"}}, "@attributes": {"alias": "GSM2395407_r2", "accession": "SRR5031956", "total_spots": "56825005", "total_bases": "17047501500", "size": "8157233978", "load_done": "true", "published": "2017-11-22 17:47:24", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR5031957", "SUBMITTER_ID": "GSM2395407_r3"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS1805844", "EXTERNAL_ID": ["SAMN06033663", "GSM2395407"]}, "@attributes": {"member_name": "", "accession": "SRS1805844", "sample_name": "GSM2395407", "sample_title": "HeLa Nucleolus Hi-C rep1", "spots": "26100640", "bases": "7830192000", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hela-n-hic-rep1_DO15081210_HF3V3CCXX_L7_1.fq.gz", "size": "2408272198", "date": "2021-02-01 20:36:26", "md5": "298a5b32692b03e4e46a16e6a8b3823e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hela-n-hic-rep1_DO15081210_HF3V3CCXX_L7_2.fq.gz", "size": "2614799750", "date": "2021-02-01 20:30:02", "md5": "dc6c9644b525165cd1bc8b3f884d618e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5031957", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5031957/SRR5031957", "size": "3778750879", "date": "2016-11-17 17:25:07", "md5": "675dadda3cdb4d35963553eec0d3f0cd", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5031957.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR005/031/SRR5031957.sralite.1", "size": "1958876235", "date": "2021-06-15 11:20:15", "md5": "a39244bce0b0093ad14fca1c8476a8b1", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "26100640"}}, "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": "7830192000"}}, "@attributes": {"alias": "GSM2395407_r3", "accession": "SRR5031957", "total_spots": "26100640", "total_bases": "7830192000", "size": "3778749652", "load_done": "true", "published": "2017-11-22 17:47:24", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]