EXPERIMENT_TITLE: GSM5692139: HiC sample replicate 1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: The Arima-HiC Kit (Arima Genomics, A510008) was used following manufacturer's protocol for low input crosslinking Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences, 21024). ). Libraries were sequenced on a NovaSeq 6000 (Illumina) in paired-end mode by the Sylvester Comprehensive Cancer Center Onco-Genomics Shared Resource.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We performed a Hi-C experiment on CD34+ cells isolated from peripheral blood and identifed topologically associated domains (TADs). Overall design: Two replicates of mobilized peripheral blood CD34+ cells were purchased from Fred Hutchinson Hematopoietic Cell Procurement Services. Hi-C was performed in replicate on CD34+ cells.
SAMPLE_TITLE: HiC sample replicate 1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Peripheral blood CD34+ cells"}, {"TAG": "tissue", "VALUE": "peripheral blood"}, {"TAG": "marker", "VALUE": "CD34 positive"}]
Pool_Member_@attributes_sample_title: HiC sample replicate 1
RUN_SET_RUN: [{"IDENTIFIERS": {"PRIMARY_ID": "SRR16956220", "SUBMITTER_ID": "GSM5692139_r1"}, "EXPERIMENT_REF": null, "RUN_ATTRIBUTES": {"RUN_ATTRIBUTE": {"TAG": "loader", "VALUE": "fastq-load.py"}}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS11080157", "EXTERNAL_ID": ["SAMN23180924", "GSM5692139"]}, "@attributes": {"member_name": "", "accession": "SRS11080157", "sample_name": "GSM5692139", "sample_title": "HiC sample replicate 1", "spots": "421441480", "bases": "127275326960", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC-1_S1_L001_R1_001.fastq.gz", "size": "30959564657", "date": "2021-11-16 18:58:41", "md5": "72222884072cad9af6e98369d5dc2d08", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC-1_S1_L001_R2_001.fastq.gz", "size": "32350030366", "date": "2021-11-16 18:46:55", "md5": "82ae286ecbe2f936e550bb09f6e4bfcf", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR16956220", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16956220/SRR16956220", "size": "40629864176", "date": "2021-11-16 19:15:56", "md5": "2438c8a2f7401935d67f15c94dccab16", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR16956220.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR016/16956/SRR16956220/SRR16956220.lite.1", "size": "32066784552", "date": "2022-10-15 01:38:53", "md5": "29a291fecbf8187d94a6024ede39f04c", "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": "421441480"}}, "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": "127275326960"}}, "@attributes": {"alias": "GSM5692139_r1", "accession": "SRR16956220", "total_spots": "421441480", "total_bases": "127275326960", "size": "40629861966", "load_done": "true", "published": "2022-11-10 21:20:05", "is_public": "true", "cluster_name": "public", "static_data_available": "1"}}, {"IDENTIFIERS": {"PRIMARY_ID": "SRR16956221", "SUBMITTER_ID": "GSM5692139_r2"}, "EXPERIMENT_REF": null, "RUN_ATTRIBUTES": {"RUN_ATTRIBUTE": {"TAG": "loader", "VALUE": "fastq-load.py"}}, "Pool": {"Member": {"IDENTIFIERS": {"PRIMARY_ID": "SRS11080157", "EXTERNAL_ID": ["SAMN23180924", "GSM5692139"]}, "@attributes": {"member_name": "", "accession": "SRS11080157", "sample_name": "GSM5692139", "sample_title": "HiC sample replicate 1", "spots": "424040410", "bases": "128060203820", "tax_id": "9606", "organism": "Homo sapiens"}}}, "SRAFiles": {"SRAFile": [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC-1_S1_L002_R1_001.fastq.gz", "size": "31134526773", "date": "2021-11-16 21:03:31", "md5": "6b9c58f1f112d30bb13f19ecc4c331eb", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "HiC-1_S1_L002_R2_001.fastq.gz", "size": "32530706012", "date": "2021-11-16 20:15:42", "md5": "ba0d740980e821b68d5645c1895854b0", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR16956221", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR16956221/SRR16956221", "size": "40855589572", "date": "2021-11-16 21:21:48", "md5": "3fe3887707d0a8cf50fd07e78c4c409f", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR16956221.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-22/SRR016/16956/SRR16956221/SRR16956221.lite.1", "size": "32264911564", "date": "2022-11-18 05:24:50", "md5": "ed077c93c18fe88e4dde6d587261f999", "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": "424040410"}}, "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": "128060203820"}}, "@attributes": {"alias": "GSM5692139_r2", "accession": "SRR16956221", "total_spots": "424040410", "total_bases": "128060203820", "size": "40855587362", "load_done": "true", "published": "2022-11-10 21:20:05", "is_public": "true", "cluster_name": "public", "static_data_available": "1"}}]