EXPERIMENT_TITLE: GSM5420224: 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": "Auxin"}]
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_IAA_HiC_1.fastq.gz", "size": "11842517088", "date": "2021-07-07 16:41:39", "md5": "7d5f90ed8dbf803d397826d5e82b2e71", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "I_IAA_HiC_2.fastq.gz", "size": "12726387432", "date": "2021-07-07 16:39:43", "md5": "f12b6cc9f2b8b8ee0b15b679530fee1e", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR15050693", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR15050693/SRR15050693", "size": "17499438196", "date": "2021-07-07 16:44:29", "md5": "1bc279255f5166aebcfa03adbf25dff1", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR15050693.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR015/15050/SRR15050693/SRR15050693.lite.1", "size": "11770197724", "date": "2022-09-27 22:00:36", "md5": "c0be47ac235c492c99920351fdc3a7fc", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]