EXPERIMENT_TITLE: GSM3262299: ME47 (eHi-C); Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For Hi-C, nuclei were extraced after fixing using a cell lysis buffer. For ChIP-seq, nuclei were extracted and chromatins were fragmented by sonication. The TF/histone-DNA complexes were isolated by antibody. All Hi-C libraries were constructed following illumina insctructions accompanying Truseq sample preparation kit.  Random indexes were introduced for eHi-C libraries to remove PCR duplication. Generally, PCR amplification was done with 7-9 cycles. All ChIP-seq libraries were generated following a ChIPmentation protocol with Nextera adapters.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Genome-wide mapping of chromatin interactions at high resolution remains experimentally and computationally challenging. Here we used a low-input “easy Hi-C” protocol to map the 3D genome architecture in human neurogenesis and brain tissues and also demonstrated that a rigorous Hi-C bias-correction pipeline (HiCorr) can significantly improve the sensitivity and robustness of Hi-C loop identification at sub-TAD level, especially the enhancer-promoter (E-P) interactions. We used HiCorr to compare the high-resolution maps of chromatin interactions from 10 tissue or cell types with a focus on neurogenesis and brain tissues. We found that dynamic chromatin loops are better hallmarks for cellular differentiation than compartment switching. HiCorr allowed direct observation of cell-type- and differentiation-specific E-P aggregates spanning large neighborhoods, suggesting a mechanism that stabilizes enhancer contacts during development. Interestingly, we concluded that Hi-C loop outperforms eQTL in explaining neurological GWAS results, revealing a unique value of high-resolution 3D genome maps in elucidating the disease etiology. Overall design: 3D genome structure mapping in human brain tissues using a newly designed easy Hi-C method
SAMPLE_TITLE: ME47 (eHi-C)
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Fetal anterior temporal cortex"}, {"TAG": "developmental stage", "VALUE": "Fetal"}, {"TAG": "tissue", "VALUE": "brain (anterior temporal cortex)"}, {"TAG": "restriction enzyme", "VALUE": "HindIII and DpnII"}]
Pool_Member_@attributes_sample_title: ME47 (eHi-C)
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR7501067", "SUBMITTER_ID": "GSM3262299_r1"}, "EXPERIMENT_REF": null, "RUN_ATTRIBUTES": {"RUN_ATTRIBUTE": [{"TAG": "loader", "VALUE": "fastq-load.py", "UNITS": null}, {"TAG": "options", "VALUE": "--appendBCtoName", "UNITS": null}]}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3528797", "EXTERNAL_ID": ["SAMN09633678", "GSM3262299"]}, "@attributes": {"member_name": "", "accession": "SRS3528797", "sample_name": "GSM3262299", "sample_title": "ME47 (eHi-C)", "spots": "335564146", "bases": "33556414600", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7501067.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR007/7501/SRR7501067/SRR7501067.lite.1", "size": "16480441551", "date": "2022-07-25 11:26:21", "md5": "4941356d1e0d5880cae17b797137bbed", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7501067", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7501067/SRR7501067", "size": "21715196203", "date": "2021-02-24 02:12:12", "md5": "3407f6c57861262896ed794d75377012", "version": "2", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ME47_Rep1_1.R2.fq", "size": "54566642284", "date": "2021-02-23 22:43:06", "md5": "d07ee8176d84b21d1d1b7d2a4c905b29", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ME47_Rep1_1.R1.fq", "size": "54566642284", "date": "2021-02-24 01:13:18", "md5": "dcfa64ab132c01f3f808318f977a873c", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "335564146"}}, "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": "33556414600"}}, "@attributes": {"alias": "GSM3262299_r1", "accession": "SRR7501067", "total_spots": "335564146", "total_bases": "33556414600", "size": "21715193992", "load_done": "true", "published": "2020-07-31 17:22:06", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR7501068", "SUBMITTER_ID": "GSM3262299_r2"}, "EXPERIMENT_REF": null, "RUN_ATTRIBUTES": {"RUN_ATTRIBUTE": [{"TAG": "loader", "VALUE": "fastq-load.py", "UNITS": null}, {"TAG": "options", "VALUE": "--appendBCtoName", "UNITS": null}]}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3528797", "EXTERNAL_ID": ["SAMN09633678", "GSM3262299"]}, "@attributes": {"member_name": "", "accession": "SRS3528797", "sample_name": "GSM3262299", "sample_title": "ME47 (eHi-C)", "spots": "385208220", "bases": "38520822000", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ME47_Rep1_2.R1.fq", "size": "62252161016", "date": "2021-02-23 22:28:58", "md5": "dc896cbd189d41cf107c2594074d37ce", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ME47_Rep1_2.R2.fq", "size": "62252161016", "date": "2021-02-24 02:30:32", "md5": "a8994b8d98f3737b99c23fc706ab2065", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7501068", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7501068/SRR7501068", "size": "26063791841", "date": "2021-02-24 03:36:58", "md5": "a620d1b5401ce11028a19d4a012d3db7", "version": "2", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7501068.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR007/7501/SRR7501068/SRR7501068.lite.1", "size": "18744882553", "date": "2022-07-21 13:18:21", "md5": "28495380ffd402fe05a363893de9ba36", "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": "385208220"}}, "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": "38520822000"}}, "@attributes": {"alias": "GSM3262299_r2", "accession": "SRR7501068", "total_spots": "385208220", "total_bases": "38520822000", "size": "26063789626", "load_done": "true", "published": "2020-07-31 17:22:06", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR7501069", "SUBMITTER_ID": "GSM3262299_r3"}, "EXPERIMENT_REF": null, "RUN_ATTRIBUTES": {"RUN_ATTRIBUTE": [{"TAG": "loader", "VALUE": "fastq-load.py", "UNITS": null}, {"TAG": "options", "VALUE": "--appendBCtoName", "UNITS": null}]}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3528797", "EXTERNAL_ID": ["SAMN09633678", "GSM3262299"]}, "@attributes": {"member_name": "", "accession": "SRS3528797", "sample_name": "GSM3262299", "sample_title": "ME47 (eHi-C)", "spots": "425132514", "bases": "42513251400", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7501069.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR007/7501/SRR7501069/SRR7501069.lite.1", "size": "20869087262", "date": "2022-07-25 11:27:31", "md5": "06b3c3b3475799461a5be00e22cb4031", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7501069", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7501069/SRR7501069", "size": "28794120662", "date": "2021-02-23 21:13:39", "md5": "9408269a88d2ee52f3fa3aae3ed6f873", "version": "2", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ME47_Rep2_1.R2.fq", "size": "68700900161", "date": "2021-02-23 21:01:47", "md5": "fc93babcd457f6d734260812db63384e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ME47_Rep2_1.R1.fq", "size": "68700900161", "date": "2021-02-23 20:49:57", "md5": "f68a22775ef4adef2578ceec4e6e72c5", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "425132514"}}, "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": "42513251400"}}, "@attributes": {"alias": "GSM3262299_r3", "accession": "SRR7501069", "total_spots": "425132514", "total_bases": "42513251400", "size": "28794118454", "load_done": "true", "published": "2020-07-31 17:22:06", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR7501070", "SUBMITTER_ID": "GSM3262299_r4"}, "EXPERIMENT_REF": null, "RUN_ATTRIBUTES": {"RUN_ATTRIBUTE": [{"TAG": "loader", "VALUE": "fastq-load.py", "UNITS": null}, {"TAG": "options", "VALUE": "--appendBCtoName", "UNITS": null}]}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3528797", "EXTERNAL_ID": ["SAMN09633678", "GSM3262299"]}, "@attributes": {"member_name": "", "accession": "SRS3528797", "sample_name": "GSM3262299", "sample_title": "ME47 (eHi-C)", "spots": "432559888", "bases": "43255988800", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7501070.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR007/7501/SRR7501070/SRR7501070.lite.1", "size": "21122461322", "date": "2022-07-25 10:34:04", "md5": "43f396992f31e277f66b725320e3cc66", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7501070", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7501070/SRR7501070", "size": "29436681482", "date": "2021-02-24 08:03:03", "md5": "fa8eb3c62787454e4d737655c73bd387", "version": "2", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ME47_Rep2_2.R2.fq", "size": "69905516562", "date": "2021-02-24 07:42:45", "md5": "84f052d4ddfb19bee4970920a23165a9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ME47_Rep2_2.R1.fq", "size": "69905516562", "date": "2021-02-24 07:25:40", "md5": "1370134baebc68e96b6f173643a4bf70", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "432559888"}}, "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": "43255988800"}}, "@attributes": {"alias": "GSM3262299_r4", "accession": "SRR7501070", "total_spots": "432559888", "total_bases": "43255988800", "size": "29436679271", "load_done": "true", "published": "2020-07-31 17:22:06", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR7501071", "SUBMITTER_ID": "GSM3262299_r5"}, "EXPERIMENT_REF": null, "RUN_ATTRIBUTES": {"RUN_ATTRIBUTE": [{"TAG": "loader", "VALUE": "fastq-load.py", "UNITS": null}, {"TAG": "options", "VALUE": "--appendBCtoName", "UNITS": null}]}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS3528797", "EXTERNAL_ID": ["SAMN09633678", "GSM3262299"]}, "@attributes": {"member_name": "", "accession": "SRS3528797", "sample_name": "GSM3262299", "sample_title": "ME47 (eHi-C)", "spots": "422668065", "bases": "42266806500", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR7501071.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR007/7501/SRR7501071/SRR7501071.lite.1", "size": "20838496528", "date": "2022-07-25 11:22:16", "md5": "41a56200a5f68f7dbfa115a3552d7e00", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR7501071", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR7501071/SRR7501071", "size": "29306822428", "date": "2021-02-24 13:02:01", "md5": "1cb3614b40f6d5c44195a1d8b9e2c2ab", "version": "2", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ME47_Rep3.R2.fq", "size": "68302002559", "date": "2021-02-24 11:50:00", "md5": "276693205951f1f0f0188a313ea663a8", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "ME47_Rep3.R1.fq", "size": "68302002559", "date": "2021-02-24 12:34:17", "md5": "e06aff4bf6a3d9cdf5f3885d035c1fc8", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]}, "CloudFiles": {"CloudFile": [null, null, null, null]}, "Statistics": {"Read": [null, null], "@attributes": {"nreads": "2", "nspots": "422668065"}}, "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": "42266806500"}}, "@attributes": {"alias": "GSM3262299_r5", "accession": "SRR7501071", "total_spots": "422668065", "total_bases": "42266806500", "size": "29306820215", "load_done": "true", "published": "2020-07-31 17:22:06", "is_public": "true", "cluster_name": "public", "has_taxanalysis": "1", "static_data_available": "1"}}]