EXPERIMENT_TITLE: GSM5420226: HiC Auxin+ rep2; 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+ rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HCT116 cells"}, {"TAG": "cell type", "VALUE": "human colorectal cancer cells"}, {"TAG": "treatment", "VALUE": "Auxin"}]
Pool_Member_@attributes_sample_title: HiC Auxin+ rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HiC Auxin+ rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "M_IAA_HiC_1.fastq.gz", "size": "12851130397", "date": "2021-07-07 20:24:48", "md5": "d51cc40a3f19c0b129dc5b613a88ed32", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "M_IAA_HiC_2.fastq.gz", "size": "14258874008", "date": "2021-07-07 20:22:33", "md5": "4412a9667788d482858858ef06ef3217", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15050695", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15050695/SRR15050695", "size": "19316792114", "date": "2021-07-07 20:30:16", "md5": "8037f4c4cca24cd85749cd2c15cd808b", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15050695.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-18/SRR015/15050/SRR15050695/SRR15050695.lite.1", "size": "12641212370", "date": "2022-07-24 12:57:58", "md5": "a77d7d7d801287d11012ce19dd62283b", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]