EXPERIMENT_TITLE: GSM2645713: Hi-C MCF-7 -E2 replicate 2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Hi-C, samples were fixed for 10 minutes with 1% formaldehyde. Fixation was stopped by adding Glycine (0.125M). Samples were frozen at -80 degee Celcius till used. In situ Hi-C was essentially performed as described(Rao et al., 2014). Briefly, for each experiment, 2 x 10E6 cells, fixed for 10 minutes with 1 % formaldehyde/PBS and washed twice with PBS, permeabilized for 7 minutes at 62°C in a PCR cycler with 200 µl lysis buffer (0.5% SDS, 50 mM Tris-HCl pH=7.5, 10 mM NaCl, 1mM EDTA, and 1X protease inhibitors solution (Roche)) and pelleted at 2500x g for 5 minutes. Supernatant was removed and nuclei were resuspended in 25 µl 10% Triton X-100, 25 µl NEB 2 buffer, 195 µl water, and rotated for 15’ at 37°C. Chromatin was digested overnight at 37°C after adding 0.5 µl 1 M DTT and 4 µl 25 U/µl Mbo I and rotated at 8 RPM. MboI was inactivated by incubation at 62°C for 20 minutes. Nuclei were centrifuged for 5 minutes at 500 x g and 200 µl supernatant was discarded. Overhangs were filled in by adding 32 μL water, 5 μl of 10X NEBuffer2, 0.35 μl of 10 mM dATP, 0.35 μl of 10 mM dTTP, 0.35 μl of 10 mM dGTP, 7.5 μl 0.4 mM Biotin-14-dCTP (Invitrogen), 4 μl 10% Triton X-100, and 5 μl of 5 U/μl Klenow enzyme (Enzymatics) and rotating for 40 minutes at room temperature. The reaction was stopped by adding 2.5 µl 0.5 M EDTA. DNA was ligated under rotation overnight at 16°C in a total volume of 400 µl ligase mix  containing 40ul 10x T4 DNA ligase buffer (Enzymatics), 36 µl 10 % Triton X-100, 5 µl 100x BSA (10 mg/ml), 1 µl (1200 U) T4 DNA ligase (Enzymatics). The reaction was terminated by adding 20 µl 0.5 M EDTA. Samples were digested for 15 minutes at 42°C with 1 µl 10 µg/µl RNase A. 33 μl of 5 M sodium chloride and 55 µl of 10% SDS were added and reverse crosslinked for 4 h at 65°C. Protein was digested with 10 μl of 20 mg/ml proteinase K (Life Technologies), incubated at 55°C for 120 minutes, shaking at 800 RPM, then 65°C for 90 minutes. DNA was extracted once with 600 µl phenol/chloroform/isoamylalcohol (25:24:1) Tris-buffered to pH 8.0 and once with 300 µl CHCl3, and precipitated overnight at -20°C with 1.5 µl 20 mg/ml glycogen and 1412 µl 100% ethanol overnight. DNA was pelleted for 20 minutes at 16000x g, 4°C and washed once with 1 ml 80% ethanol for 5 minutes, 8000x g, 4°C. Pellets were dissolved in 131 µl TT (0.05% Tween 20/10 mM Tris pH=8) each. DNA was sheared with 300 bp Covaris protocol in snap cap tube in a Covaris E220 at 10 % duty cycle, intensity 140 W, 200 cycles/burst for 80” total time. Large DNA fragments (>400 bp) were depleted with 5 µl Speedbeads and 6.45% PEG8000/2.5 M NaCl. Supernatant was transferred to fresh tubes and small DNA fragments were collected with 9.5% PEG8000 by adding an additional 60 µl PEG8000/2.5 M NaCl and 3 µl Speedbeads. DNA was eluted in 50ul TT for 5 minutes. DNA was captured with 50 µl 2x B&W buffer containing 0.2 % Tween 20 and 15 µl T1 Dynabeads (Invitrogen, washed twice with 1x B&W buffer (10 mM Tris-HCl pH 7.5, 01 mM EDTA, 2 M NaCl, then suspended in 51 µl 2x B&W buffer containing 0.2% Tween 20), rotating for 30 minutes at room temperature. Beads were washed once with 500 µl each of 1x B&W/0.1 % Triton-X100, once with TET (0.05% Tween 20/TE). Hi-C library bound to beads were resuspend in 100 µl end repair mix (KAPA Library Preparation for Illumina) Incubated for 30 minutes at 20°C. Reaction was stopped by adding 2.5 µl 0.5 M EDTA. Beads were collected and washed twice with 150 µl 1x B&W/0.1% Triton-X100, once with 180 µl TET. Beads were resuspend in 50 ul A-tailing reaction mix (KAPA Library Preparation for Illumina), incubated 30 minutes at 30°C. Reaction was stopped by adding 1.5 µl 0.5 M EDTA. Beads were collected and washed twice with 150 µl 1x B&W/0.1% Triton-X100, once with 180 µl TET. Sequencing adapters were ligated to the bead-bound DNA in 100 µl 1x rapid ligation buffer (Enzymatics) containing 0.1% Tween 20,  2ul 1:20 Truseq adapters (Illumina), 1 µl (3000 U) T4 DNA ligase (Enzymatics) for 20 minutes at room temperature. The reaction was stopped with 5 µl 0.5 M EDTA, beads washed twice with 1x B&W, twice with 0.1% Tween 20/TE, then resuspended in 30 µl 0.033% Tween20/LoTE, (TE diluted 1:4 with water). Libraries were PCR-amplified using the 10 µl of the bead suspension as template for 10 cycles using KAPA HiFi, size-selected to 225-425 bp insert size using speedbeads PEG8000/2.5 M NaCl solutions, and paired-end sequenced on an Illumina HiSeq 2500.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Detailed analysis of estrogen mediated enhancer landscape and chromosomal architectural changes specifically in human chromosome 21. Overall design: in situ Hi-C experiments are designed to elucidate 3D chromatin landscape in human breast cancer cells (MCF7) under basal and estrogen treated conditions.
SAMPLE_TITLE: Hi-C MCF-7 -E2 replicate 2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Hi-C MCF-7 -E2"}, {"TAG": "cell line", "VALUE": "MCF7"}, {"TAG": "cell type", "VALUE": "Human breast cancer cells"}, {"TAG": "genotype/variation", "VALUE": "wild type"}, {"TAG": "treated with", "VALUE": "ICI 182,780, an estrogen receptor alpha antagonist; Control"}]
Pool_Member_@attributes_sample_title: Hi-C MCF-7 -E2 replicate 2
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR5638509", "SUBMITTER_ID": "GSM2645713_r1"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS2246323", "EXTERNAL_ID": ["SAMN07184414", "GSM2645713"]}, "@attributes": {"member_name": "", "accession": "SRS2246323", "sample_name": "GSM2645713", "sample_title": "Hi-C MCF-7 -E2 replicate 2", "spots": "4000000", "bases": "400000000", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R1_001.fastq.gz", "size": "200687441", "date": "2020-03-26 12:18:12", "md5": "be197a4324db6622ce4657817ac0be8b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R2_001.fastq.gz", "size": "208941444", "date": "2020-03-26 15:18:53", "md5": "0886a88d9dae695bc99cf9bd7154bffc", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5638509", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5638509/SRR5638509", "size": "241065397", "date": "2017-06-01 11:46:20", "md5": "4d78de87a8e9e2eadd0360784dc52948", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5638509.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/638/SRR5638509.sralite.1", "size": "108732100", "date": "2020-06-24 00:57:41", "md5": "eaae19ac31b37f6b276b7a06e5170d19", "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": "4000000"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "400000000"}}, "@attributes": {"alias": "GSM2645713_r1", "accession": "SRR5638509", "total_spots": "4000000", "total_bases": "400000000", "size": "241063647", "load_done": "true", "published": "2019-02-13 18:27:36", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR5638510", "SUBMITTER_ID": "GSM2645713_r10"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS2246323", "EXTERNAL_ID": ["SAMN07184414", "GSM2645713"]}, "@attributes": {"member_name": "", "accession": "SRS2246323", "sample_name": "GSM2645713", "sample_title": "Hi-C MCF-7 -E2 replicate 2", "spots": "3848177", "bases": "384817700", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5638510", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5638510/SRR5638510", "size": "221780494", "date": "2017-06-01 11:47:36", "md5": "c44573869df7299938d539d6e653cd07", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5638510.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/638/SRR5638510.sralite.1", "size": "104499537", "date": "2020-06-21 11:22:57", "md5": "cd38546af43c51b81bcf773ef6ab5333", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R2_010.fastq.gz", "size": "194696342", "date": "2020-03-26 11:48:01", "md5": "3fdf18e11b7daed366791bb8bf46a326", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R1_010.fastq.gz", "size": "187141743", "date": "2020-03-26 15:51:03", "md5": "0b690147d1f5deae9e05e80839f38ad2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "3848177"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "384817700"}}, "@attributes": {"alias": "GSM2645713_r10", "accession": "SRR5638510", "total_spots": "3848177", "total_bases": "384817700", "size": "221778743", "load_done": "true", "published": "2019-02-13 18:27:36", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR5638511", "SUBMITTER_ID": "GSM2645713_r11"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS2246323", "EXTERNAL_ID": ["SAMN07184414", "GSM2645713"]}, "@attributes": {"member_name": "", "accession": "SRS2246323", "sample_name": "GSM2645713", "sample_title": "Hi-C MCF-7 -E2 replicate 2", "spots": "20711143", "bases": "2071114300", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0012_R1_001.fastq.gz", "size": "788361888", "date": "2020-03-26 12:18:12", "md5": "3b631d93c6d81033ce5a584511e8ef09", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0012_R2_001.fastq.gz", "size": "811054488", "date": "2020-03-26 12:18:12", "md5": "77736ce399be2efed428db70955dd61b", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5638511", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5638511/SRR5638511", "size": "910084518", "date": "2017-06-01 11:53:28", "md5": "e9cb380b1ec19f611430f7c36920f671", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5638511.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/638/SRR5638511.sralite.1", "size": "522858490", "date": "2020-06-24 01:00:53", "md5": "6ac752b36f2b7fe9c639fb0ee21efa0f", "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": "20711143"}}, "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": "2071114300"}}, "@attributes": {"alias": "GSM2645713_r11", "accession": "SRR5638511", "total_spots": "20711143", "total_bases": "2071114300", "size": "910082989", "load_done": "true", "published": "2019-02-13 18:27:36", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR5638512", "SUBMITTER_ID": "GSM2645713_r12"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS2246323", "EXTERNAL_ID": ["SAMN07184414", "GSM2645713"]}, "@attributes": {"member_name": "", "accession": "SRS2246323", "sample_name": "GSM2645713", "sample_title": "Hi-C MCF-7 -E2 replicate 2", "spots": "20645366", "bases": "2064536600", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0012_R1_002.fastq.gz", "size": "779250904", "date": "2020-03-26 16:21:09", "md5": "63a9329d7e8ed86f4b593497da37d7cb", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0012_R2_002.fastq.gz", "size": "801914495", "date": "2020-03-26 15:51:13", "md5": "fbb69f1f44e4bc265f6d82b244ee316e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5638512", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5638512/SRR5638512", "size": "897652556", "date": "2017-06-01 11:55:04", "md5": "4a6ec1b425f7294b72829c40342a3bd8", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5638512.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/638/SRR5638512.sralite.1", "size": "521210680", "date": "2021-06-15 16:53:03", "md5": "bbd1e2363452f611f60c2acb352bbe85", "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": "20645366"}}, "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": "2064536600"}}, "@attributes": {"alias": "GSM2645713_r12", "accession": "SRR5638512", "total_spots": "20645366", "total_bases": "2064536600", "size": "897651022", "load_done": "true", "published": "2019-02-13 18:27:36", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR5638513", "SUBMITTER_ID": "GSM2645713_r2"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS2246323", "EXTERNAL_ID": ["SAMN07184414", "GSM2645713"]}, "@attributes": {"member_name": "", "accession": "SRS2246323", "sample_name": "GSM2645713", "sample_title": "Hi-C MCF-7 -E2 replicate 2", "spots": "4000000", "bases": "400000000", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R1_002.fastq.gz", "size": "201330146", "date": "2020-03-26 12:18:12", "md5": "9907172192dc8fa90be0ad4dc4caaf40", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R2_002.fastq.gz", "size": "209746237", "date": "2020-03-26 16:19:24", "md5": "6c1dbb487e71329138301c289f86ef30", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5638513", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5638513/SRR5638513", "size": "242239555", "date": "2017-06-01 11:46:26", "md5": "937b9081c1f0e60f9af44a4d40ec76b3", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5638513.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/638/SRR5638513.sralite.1", "size": "108745820", "date": "2020-06-24 00:57:42", "md5": "9aedcb4bcb1109987ca30e6dccb43993", "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": "4000000"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "400000000"}}, "@attributes": {"alias": "GSM2645713_r2", "accession": "SRR5638513", "total_spots": "4000000", "total_bases": "400000000", "size": "242237808", "load_done": "true", "published": "2019-02-13 18:27:36", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR5638514", "SUBMITTER_ID": "GSM2645713_r3"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS2246323", "EXTERNAL_ID": ["SAMN07184414", "GSM2645713"]}, "@attributes": {"member_name": "", "accession": "SRS2246323", "sample_name": "GSM2645713", "sample_title": "Hi-C MCF-7 -E2 replicate 2", "spots": "4000000", "bases": "400000000", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R1_003.fastq.gz", "size": "193320956", "date": "2020-03-26 12:18:12", "md5": "5e41fe5a4899a232ad461b820f8cb8f8", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R2_003.fastq.gz", "size": "202047016", "date": "2020-03-26 12:18:12", "md5": "8e7e2fbc7629016d6499228d69f3be7a", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5638514", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5638514/SRR5638514", "size": "229384223", "date": "2017-06-01 11:46:19", "md5": "5701ecd51f1d82f189f51c4a82dec918", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5638514.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/638/SRR5638514.sralite.1", "size": "108686880", "date": "2020-06-24 00:57:43", "md5": "bff513a9e95afead2394fdcf91ab44d7", "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": "4000000"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "400000000"}}, "@attributes": {"alias": "GSM2645713_r3", "accession": "SRR5638514", "total_spots": "4000000", "total_bases": "400000000", "size": "229382478", "load_done": "true", "published": "2019-02-13 18:27:36", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR5638515", "SUBMITTER_ID": "GSM2645713_r4"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS2246323", "EXTERNAL_ID": ["SAMN07184414", "GSM2645713"]}, "@attributes": {"member_name": "", "accession": "SRS2246323", "sample_name": "GSM2645713", "sample_title": "Hi-C MCF-7 -E2 replicate 2", "spots": "4000000", "bases": "400000000", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R2_004.fastq.gz", "size": "198903595", "date": "2020-03-26 18:19:47", "md5": "6f97a55d7be0baa8c64285f62d09c261", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5638515", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5638515/SRR5638515", "size": "224424555", "date": "2017-06-01 11:46:25", "md5": "80c4aa9679e91b570f41b197a516b7e2", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5638515.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/638/SRR5638515.sralite.1", "size": "108625352", "date": "2020-06-24 00:57:49", "md5": "1aeeb9429014a2f647e97a91b0e3611b", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R1_004.fastq.gz", "size": "190412985", "date": "2020-03-26 16:20:57", "md5": "ce6ffac8f801851fabcb56266353d4b9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "4000000"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "400000000"}}, "@attributes": {"alias": "GSM2645713_r4", "accession": "SRR5638515", "total_spots": "4000000", "total_bases": "400000000", "size": "224422808", "load_done": "true", "published": "2019-02-13 18:27:36", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR5638516", "SUBMITTER_ID": "GSM2645713_r5"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS2246323", "EXTERNAL_ID": ["SAMN07184414", "GSM2645713"]}, "@attributes": {"member_name": "", "accession": "SRS2246323", "sample_name": "GSM2645713", "sample_title": "Hi-C MCF-7 -E2 replicate 2", "spots": "3849192", "bases": "384919200", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R1_005.fastq.gz", "size": "186249086", "date": "2020-03-26 16:20:58", "md5": "852c6cd40e39927b3559d3253eed2587", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5638516", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5638516/SRR5638516", "size": "220763527", "date": "2017-06-01 11:46:30", "md5": "348b7041c825ee98a3bc57b93e136ab8", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5638516.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/638/SRR5638516.sralite.1", "size": "104509330", "date": "2021-06-14 18:43:39", "md5": "e08acb3a3a002ec88876b4c084353e17", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R2_005.fastq.gz", "size": "194220494", "date": "2020-03-26 10:19:17", "md5": "e6489669ecd3deb5aa0d5f6ecb89a223", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "3849192"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "384919200"}}, "@attributes": {"alias": "GSM2645713_r5", "accession": "SRR5638516", "total_spots": "3849192", "total_bases": "384919200", "size": "220761777", "load_done": "true", "published": "2019-02-13 18:27:36", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR5638517", "SUBMITTER_ID": "GSM2645713_r6"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS2246323", "EXTERNAL_ID": ["SAMN07184414", "GSM2645713"]}, "@attributes": {"member_name": "", "accession": "SRS2246323", "sample_name": "GSM2645713", "sample_title": "Hi-C MCF-7 -E2 replicate 2", "spots": "4000000", "bases": "400000000", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R1_006.fastq.gz", "size": "201721952", "date": "2020-03-26 14:24:28", "md5": "244add1035d6f84007dfd5d65cb588f2", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R2_006.fastq.gz", "size": "209615892", "date": "2020-03-26 18:19:47", "md5": "a64951b25afd8d9df6589923c3c5112f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5638517", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5638517/SRR5638517", "size": "242423697", "date": "2017-06-01 11:46:31", "md5": "74472d2c986d90cd90aa6add7734bbf0", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5638517.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/638/SRR5638517.sralite.1", "size": "108759364", "date": "2020-06-24 00:58:13", "md5": "9923376aa151a6e15f4f14a954186b69", "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": "4000000"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "400000000"}}, "@attributes": {"alias": "GSM2645713_r6", "accession": "SRR5638517", "total_spots": "4000000", "total_bases": "400000000", "size": "242421952", "load_done": "true", "published": "2019-02-13 18:27:36", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR5638518", "SUBMITTER_ID": "GSM2645713_r7"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS2246323", "EXTERNAL_ID": ["SAMN07184414", "GSM2645713"]}, "@attributes": {"member_name": "", "accession": "SRS2246323", "sample_name": "GSM2645713", "sample_title": "Hi-C MCF-7 -E2 replicate 2", "spots": "4000000", "bases": "400000000", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R1_007.fastq.gz", "size": "202998674", "date": "2020-03-26 16:21:02", "md5": "8964ec40573c5e98d64527e79f4e7c31", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R2_007.fastq.gz", "size": "210919678", "date": "2020-03-26 18:19:47", "md5": "0e7a2f2925898eefb74016fa18c23adb", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5638518", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5638518/SRR5638518", "size": "244501629", "date": "2017-06-01 11:46:58", "md5": "3f7c5dc89ae04b2553b82f5c42dddd0d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5638518.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/638/SRR5638518.sralite.1", "size": "108762140", "date": "2021-06-14 18:43:41", "md5": "aec5a269938ab138015f1a6cc4b0b454", "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": "4000000"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "400000000"}}, "@attributes": {"alias": "GSM2645713_r7", "accession": "SRR5638518", "total_spots": "4000000", "total_bases": "400000000", "size": "244499882", "load_done": "true", "published": "2019-02-13 18:27:36", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR5638519", "SUBMITTER_ID": "GSM2645713_r8"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS2246323", "EXTERNAL_ID": ["SAMN07184414", "GSM2645713"]}, "@attributes": {"member_name": "", "accession": "SRS2246323", "sample_name": "GSM2645713", "sample_title": "Hi-C MCF-7 -E2 replicate 2", "spots": "4000000", "bases": "400000000", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R1_008.fastq.gz", "url": "https://sra-pub-src-1.s3.amazonaws.com/SRR5638519/hic-0000-0004_R1_008.fastq.gz.1", "size": "194975959", "date": "2020-03-26 12:18:12", "md5": "30a7e195555b20b918d2ccf8965ce814", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null], "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R2_008.fastq.gz", "url": "https://sra-pub-src-1.s3.amazonaws.com/SRR5638519/hic-0000-0004_R2_008.fastq.gz.1", "size": "203285456", "date": "2020-03-26 18:19:47", "md5": "be5db91f09b7caf1bc80b8ae543da441", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5638519.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/638/SRR5638519.sralite.1", "size": "108682612", "date": "2021-06-15 16:52:04", "md5": "e720dc8ae16e1ef721df9979a74134d2", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]}, "CloudFiles": {"CloudFile": [null, null, null]}, "@attributes": {"alias": "GSM2645713_r8", "accession": "SRR5638519", "total_spots": "4000000", "total_bases": "400000000", "size": "231768129", "load_done": "true", "published": "2019-02-13 18:27:36", "is_public": "true", "cluster_name": "public", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR5638520", "SUBMITTER_ID": "GSM2645713_r9"}, "EXPERIMENT_REF": null, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS2246323", "EXTERNAL_ID": ["SAMN07184414", "GSM2645713"]}, "@attributes": {"member_name": "", "accession": "SRS2246323", "sample_name": "GSM2645713", "sample_title": "Hi-C MCF-7 -E2 replicate 2", "spots": "4000000", "bases": "400000000", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R1_009.fastq.gz", "size": "192465264", "date": "2020-03-26 12:18:12", "md5": "8caec4c7641ae3ff7db9671dff31a586", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "hic-0000-0004_R2_009.fastq.gz", "size": "200459478", "date": "2020-03-26 14:23:42", "md5": "99a47c0eddbbd1b6a13fa39d0ffd9219", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5638520", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5638520/SRR5638520", "size": "227254989", "date": "2017-06-01 11:47:01", "md5": "1aac53c3f0702d15fab4c55499fe9d3b", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5638520.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/638/SRR5638520.sralite.1", "size": "108616848", "date": "2021-06-15 05:35:31", "md5": "dca2937500483ca7d703c39ca82ded6f", "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": "4000000"}}, "Bases": {"Base": [null, null, null, null, null], "@attributes": {"cs_native": "false", "count": "400000000"}}, "@attributes": {"alias": "GSM2645713_r9", "accession": "SRR5638520", "total_spots": "4000000", "total_bases": "400000000", "size": "227253243", "load_done": "true", "published": "2019-02-13 18:27:36", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]