EXPERIMENT_TITLE: GSM5420223: HiC Auxin- rep1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Fixed chromatin was digested using DpnⅡ enzyme, followed by biotin incorporation with Biotin-14-dATP. After DNA ligation, DNA was sonicated and captured with Streptavidin C-1 beads. Libraries were prepared using Nextera DNA library preparation kit according to manufacturer's instructions. DNA was amplified using Nextera PCR primers. Libraries were purified using SPRI AMPureXP beads and were paired-end sequenced on Illumina HiSeq2500 platform
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Identification of the genome-wide pair-wise chromatin interaction in Auxin untreated and Auxin treated HCT116 CTCF Degron cells. Overall design: Examination of genome-wide chromatin interaction in WT and CTCF KD HCT116 colorectal cancer cells
SAMPLE_TITLE: HiC Auxin- rep1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HCT116 cells"}, {"TAG": "cell type", "VALUE": "human colorectal cancer cells"}, {"TAG": "treatment", "VALUE": "untreated"}]
Pool_Member_@attributes_sample_title: HiC Auxin- rep1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC Auxin- rep1
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "I_Con_HiC_1.fastq.gz", "size": "11442706098", "date": "2021-07-07 08:00:37", "md5": "ec3344392103727471cb48d9eb138353", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "I_Con_HiC_2.fastq.gz", "size": "12623597867", "date": "2021-07-07 08:03:48", "md5": "30904408bcdedd8f2ee3b94e703ca57f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15050692", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15050692/SRR15050692", "size": "17148371667", "date": "2021-07-07 08:09:16", "md5": "47c1ea51531fa51ee166e31c8eb9f590", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15050692.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-18/SRR015/15050/SRR15050692/SRR15050692.lite.1", "size": "11151386823", "date": "2022-07-24 12:35:52", "md5": "8a2e079c11f0e7c53e743483ccbbf497", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]