EXPERIMENT_TITLE: GSM6671999: HEK293T cells, Hi-C, R617Q; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cells were lysed in lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA-630) and digested in 100 U Mbo I restriction enzyme (NEB) at 37 °C overnight. The DNA ends were marked with biotin-labeled dATPs, and the 5' overhang was filled using the Klenow enzyme. The blunt ends were ligated with T4 DNA ligase for 4 h at RT. Crude DNA was fragmented into ~400 bp fragments, and biotinylated DNA was pulled down with C1 streptavidin beads. For library preparation, approximately 500 ng of bead DNA was used as the initial material and amplified 5 cycles after adapter ligation.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: To investigate the effect of MED23 R617Q mutation on gene regulation, we established MED23/R617Q mutant HEK293T cell line. Overall design: Comparative chromain interation analysis of Hi-C data for the WT and MED23/R617Q mutant HEK293T cells.
SAMPLE_TITLE: HEK293T cells, Hi-C, R617Q
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "HEK293T"}, {"TAG": "cell line", "VALUE": "HEK293T"}, {"TAG": "cell type", "VALUE": "Human embryonic kidney cells"}, {"TAG": "genotype", "VALUE": "MED23/R617Q"}]
Pool_Member_@attributes_sample_title: HEK293T cells, Hi-C, R617Q
RUN_SET_RUN_Pool_Member_@attributes_sample_title: HEK293T cells, Hi-C, R617Q
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR22020404.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos4/sra-pub-zq-3/SRR022/22020/SRR22020404/SRR22020404.lite.1", "size": "28693876856", "date": "2023-05-08 14:32:06", "md5": "b4b39e939332a70649ae4690f85d920a", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR22020404", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR22020404/SRR22020404", "size": "47600644532", "date": "2022-10-24 21:29:10", "md5": "443245b1ec6161577cb86707814dc561", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_R617Q-2.fastq.gz", "size": "33469286573", "date": "2022-10-24 21:15:05", "md5": "5c361cd7fdc97729f279e1f5d02463e5", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "Hi-C_R617Q-1.fastq.gz", "size": "30983415446", "date": "2022-10-24 21:17:12", "md5": "6163e9646f50a0be6eac66af39285a93", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]