EXPERIMENT_TITLE: GSM4061356: BJ5ta_24hr_R1_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Briefly, 5-20 million cells were fixed with 1% formaldehyde, suspended in cell lysis buffer for permeabilization, and homogenized by douncing. Crosslinked chromatin was digested overnight with HindIII. Sticky ends were filled in with biotin-dCTP, and the blunt ends of interacting fragments were ligated together. DNA was purified by two phenol-chloroform extractions and ethanol precipitation. Biotin-dCTP at unligated ends was removed, and the DNA was sheared to a target size of 200-400 bp by a Covaris sonicator Biotinylated DNA was pulled down using streptavidin coated magnetic beads and prepared for multiplex sequencing on an Illumina platform using the NEBNext Ultra II kit (NEB). All end preparation, adaptor ligation, and PCR amplification steps were carried out on bead bound DNA libraries.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We investigate the impact of DNA damage response and repair on 3D genome folding using Hi-C experiments on wild type cells and ataxia telangiectasia mutated (ATM) patient cells. Fibroblasts, lymphoblasts, and ATM-deficient fibroblasts were irradiated with 5 Gy X-rays and Hi-C was performed after 30 minutes, 24 hours, or 5 days after irradiation. Overall design: Examination of the effects of X-rays on 6 different cell types
SAMPLE_TITLE: BJ5ta_24hr_R1_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "BJ5ta_24hr"}, {"TAG": "cell line", "VALUE": "BJ5ta"}, {"TAG": "cell type", "VALUE": "Foreskin fibroblast"}, {"TAG": "condition", "VALUE": "24hr"}, {"TAG": "media", "VALUE": "4:1DMEM:Medium199,10%FBS, 0.01mgHygroB"}]
Pool_Member_@attributes_sample_title: BJ5ta_24hr_R1_HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: BJ5ta_24hr_R1_HiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR10070524.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR010/10070/SRR10070524/SRR10070524.lite.1", "size": "11257855643", "date": "2022-07-05 12:28:39", "md5": "aa780b89b7f833fc42676b21c37a1945", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR10070524", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR10070524/SRR10070524", "size": "13250553987", "date": "2019-09-05 13:01:51", "md5": "8ce09ed43a1af5130e3e9ebad5e97a9c", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Xray-BJ5ta-24hr-R1_S3_L001_R2_001.fastq.gz", "size": "11853659295", "date": "2019-09-05 12:53:50", "md5": "9de8b798e60821fbe9dd50ab47892914", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Xray-BJ5ta-24hr-R1_S3_L001_R1_001.fastq.gz", "size": "11616145251", "date": "2019-09-05 12:48:11", "md5": "2031032f8d196744db45354f95217abc", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]