EXPERIMENT_TITLE: GSM7457945: A673 ARID1A WT RE3 in situ Hi-C; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: The harvested 1 million cells were crosslinked with 1% formaldehyde for 9 min at RT in 10 ml PBS and 100 µl FBS. Cells were treated with 250 mM glycine for 5 min at RT and 15 min on ice, to quench the crosslinking. The cells were then lysed with 10 nM Tris-HCl pH 8, 10 mM NaCl, and 0.2% IGEPAL CA630. The crosslinked chromatin was digested with 100 U MboI, labeled with biotin-14-dTCP, and ligated with T4 DNA Ligase. The ligated samples were reverse-crosslinked with 2 µg/µl proteinase K, 1% SDS, and 500 mM NaCl overnight at 65ºC. The DNA fragments were collected with Ampure XP beads (Beckman Coulter, A63881) and sonicated using Covaris S220 into 300~400bp. The biotin-labeled DNA was pulled down with Dynabeads MyOne streptavidin T1 beads (Invitrogen, 65602) with thorough washings. DNA end repair, un-ligated ends removal, adenosine addition at 3' end (NEB, M0212), ligation of Illumina indexed adapters (NEB, M2200), and PCR amplification was performed to generate Hi-C libraries. The generated libraries were sequenced in 100 bp paired-end mode.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We charaterized the effect of ARID1A phase separation on transcriptome/epigenome/3D chromatin structure in Ewing's Sarcoma cancer cell line Overall design: RNA-seq and ATAC-seq were performed on 6 ARID1A LLPS-positive and 7 ARID1A LLPS-negative A673 cell lines. In situ Hi-C was performed on 2 ARID1A LLPS-positive and 2 negative A673 cell lines.
SAMPLE_TITLE: A673 ARID1A WT RE3 in situ Hi-C
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "A673"}, {"TAG": "cell line", "VALUE": "A673"}, {"TAG": "genotype", "VALUE": "ARID1A WT"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: A673 ARID1A WT RE3 in situ Hi-C
RUN_SET_RUN_Pool_Member_@attributes_sample_title: A673 ARID1A WT RE3 in situ Hi-C
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A673.RE-3.HiC_1.fq.gz", "size": "37765454840", "date": "2023-06-07 01:11:02", "md5": "37f52023415b1bbb2398adf090523457", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "A673.RE-3.HiC_2.fq.gz", "size": "37297026474", "date": "2023-06-07 01:13:30", "md5": "c06b8ed88697ea5a8a214d928d8d267d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR24837354", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR24837354/SRR24837354", "size": "55879647554", "date": "2023-06-07 01:35:17", "md5": "d41bad5c25dde40f06fcb8613be16dff", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR24837354.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos6/sra-pub-zq-40/SRR024/24837/SRR24837354/SRR24837354.lite.1", "size": "21172483239", "date": "2023-06-12 06:44:54", "md5": "bbfc79cf1da284e2ebd4653c8b5bbb60", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]