EXPERIMENT_TITLE: GSM5350058: BERP35T4C [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: BERP35T4C [Hi-C]
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "bronchial epithelium"}, {"TAG": "cell line", "VALUE": "BERP35T4"}, {"TAG": "tissue", "VALUE": "bronchial epithelium"}]
Pool_Member_@attributes_sample_title: BERP35T4C [Hi-C]
RUN_SET_RUN_Pool_Member_@attributes_sample_title: BERP35T4C [Hi-C]
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR14698235.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pub-zq-24/SRR014/14698/SRR14698235/SRR14698235.lite.1", "size": "4363478784", "date": "2023-02-04 13:26:20", "md5": "672f958eacaa05a2cdeba065d706cea3", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR14698235", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR14698235/SRR14698235", "size": "8411397034", "date": "2021-06-05 09:05:54", "md5": "ae513ab0b25262b9394ef5e1acb12f6f", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "BERP35T4C_hg19.bwt2pairs.sorted.bam.bam", "size": "22774032610", "date": "2021-06-05 08:55:06", "md5": "a9bbb240426d580eac2cd7a201e1b7d8", "version": "1", "semantic_name": "bam", "supertype": "Original", "sratoolkit": "0"}}]