EXPERIMENT_TITLE: GSM5350053: BERP35T1A [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: BERP35T1A [Hi-C]
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "bronchial epithelium"}, {"TAG": "cell line", "VALUE": "BERP35T1"}, {"TAG": "tissue", "VALUE": "bronchial epithelium"}]
Pool_Member_@attributes_sample_title: BERP35T1A [Hi-C]
RUN_SET_RUN_Pool_Member_@attributes_sample_title: BERP35T1A [Hi-C]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR14698230.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR014/14698/SRR14698230/SRR14698230.lite.1", "size": "1759588324", "date": "2023-02-06 18:40:13", "md5": "6137e3ce61f7d7f6f3fc332cbae30bf9", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR14698230", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14698230/SRR14698230", "size": "5623168589", "date": "2021-06-02 05:39:42", "md5": "3de438d287ef6707d3384685d3736312", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "BERP35T1A_hg19.bwt2pairs.sorted.bam.bam", "size": "12746353096", "date": "2021-06-02 05:33:44", "md5": "26348d271b8d0587870a11ff3da72864", "version": "1", "semantic_name": "bam", "supertype": "Original", "sratoolkit": "0"}}]