EXPERIMENT_TITLE: GSM3930295: SW480-2_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: In situ HiC was performed as described previously (Rao et al., 2014).  In brief, crosslinked cells or tumor were thawed on ice in HiC lysis buffer. Tissue samples were mechanically disrupted with the Biomasher tissue grinder (Kimble Chase).  Tissue and cell line samples were permeabilized in 0.5% SDS at 37 degrees, quenched with Triton X100 and chromatin was digested with 100-200U MboI at 37 degrees overnight.  Nuclei were then pelleted, ends were marked with biotin-14-dATP (ThermoFisher 19524016) and chromatin was ligated for 5 hours by T4 DNA ligase (M0202).  Samples were treated with proteinase K at 55 degrees for 30 minutes and cross-links were reversed at 68 degrees overnight.  DNA was ethanol precipitated and sheared on a Covaris LE220 as per Rao et al., 2014.  DNA was cleaned up via AMPure XP beads (Beckman Coulter, A63881) and quantified by Qubit dsDNA High Sensitivity Assay (Life Technologies, Q32854).  Samples were bound to Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602) and washed.  End repair, dATP attachment and adapter ligation was performed.  Final PCR amplification was performed using barcoded sequencing primers and PCR.  Libraries were purified using AMPure XP beads and sequenced on either a NextSeq500 (150 cycle kit) or the HiSeq2500 (high output; 200 cycle kit).
STUDY_DESCRIPTOR_STUDY_ABSTRACT: To understand how nuclear architecture is altered in cancer, we profiled genome topology along with DNA methylation, chromatin modifications and the DNA binding factors CTCF in primary colon tumors, normal colon and colon cancer cell lines. Overall design: Samples include colon cancer cell lines (HCT116, SW480, RKO, LS-174T), a line derived from normal colon (FHC) and patient biopsies. The raw data from the in vitro models can be found through SRA. Due to patient privacy concerns, raw data for patient samples have been submitted to dbGAP (accession phs002288.v1.p1).
SAMPLE_TITLE: SW480-2_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Cell line"}, {"TAG": "tissue", "VALUE": "SW480 Cell line"}, {"TAG": "biological sample", "VALUE": "SW480"}, {"TAG": "treatment", "VALUE": "NA"}]
Pool_Member_@attributes_sample_title: SW480-2_HiC
RUN_SET_RUN_Pool_Member_@attributes_sample_title: SW480-2_HiC
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SW480-2_hic_R1.fastq.gz", "size": "15052644332", "date": "2019-07-12 17:01:10", "md5": "3d76b4ff99ec77aeb61fdf3bfeedd4aa", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SW480-2_hic_R2.fastq.gz", "size": "17736538444", "date": "2019-07-12 17:06:30", "md5": "1b261b0956a95efdb591ddab804e0f45", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR9675764", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR9675764/SRR9675764", "size": "21707774931", "date": "2019-07-12 17:14:02", "md5": "37d945dc658f79c1d0fd844ed95c9721", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR9675764.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/SRR009/9675/SRR9675764/SRR9675764.lite.1", "size": "12493441119", "date": "2022-06-23 10:24:56", "md5": "55c4bfcf08d177e536083b709784ef0e", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]