EXPERIMENT_TITLE: GSM5350050: BEP2DA [Hi-C]; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Nuclei were extracted and the chromatin was applied with 4 cutter restriction enzyme (400 units MboI). The next steps included making the DNA ends with biotin-14-dCTP and performing blunt-end ligation of crosslinked fragments. Finally, after shearing to approximately 200-600 bp by sonication, the libraries were constructed through end-repair, A-tailing, adapter ligation and amplifying.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: we generated ATAC-seq, RNA-seq and high-resolution Hi-C datasets for finer-scale dissection of chromatin architecture alterations in radiation induced malignant transformation of bronchial epithelial cells. Overall design: The Hi-C profiles of normal human bronchial epithelial cells and radiation induced lung cancer cells
SAMPLE_TITLE: BEP2DA [Hi-C]
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "bronchial epithelium"}, {"TAG": "cell line", "VALUE": "BEP2D"}, {"TAG": "tissue", "VALUE": "bronchial epithelium"}]
Pool_Member_@attributes_sample_title: BEP2DA [Hi-C]
RUN_SET_RUN_Pool_Member_@attributes_sample_title: BEP2DA [Hi-C]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR14698227.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-zq-38/SRR014/14698/SRR14698227/SRR14698227.lite.1", "size": "3913684542", "date": "2022-10-17 16:13:33", "md5": "66426f4d5b7a3c8e632f7d1c8db027a2", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR14698227", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14698227/SRR14698227", "size": "7214981028", "date": "2021-06-03 22:15:48", "md5": "298f7ecb1a1c1d364a19cf2124ef79e8", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "BEP2DA_hg19.bwt2pairs.sorted.bam.bam", "size": "20521882520", "date": "2021-06-03 22:05:29", "md5": "306c85abd700012407eb71c42c1e5da2", "version": "1", "semantic_name": "bam", "supertype": "Original", "sratoolkit": "0"}}]