EXPERIMENT_TITLE: GSM5420225: 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": "untreated"}]
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_Con_HiC_1.fastq.gz", "size": "12092732056", "date": "2021-07-07 16:34:19", "md5": "4b45ebc009834a391ae946e459fb76c7", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "M_Con_HiC_2.fastq.gz", "size": "13147208487", "date": "2021-07-07 16:37:50", "md5": "d113436e005e7b0e9cab12681581bae9", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15050694", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15050694/SRR15050694", "size": "17983273222", "date": "2021-07-07 16:42:05", "md5": "0e69d8e55d5908c3293e0a029ca3d43d", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15050694.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-18/SRR015/15050/SRR15050694/SRR15050694.lite.1", "size": "12078137558", "date": "2022-07-24 12:57:01", "md5": "0f05536a264c72186b7db54e201e4e3b", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]