EXPERIMENT_TITLE: GSM6203840: C42B, HiC, rep2; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: The human prostate cancer C42B cells were obtained from ViroMed Laboratories (Minneapolis, MN, USA) Cells were grown at 37 °C in 5% CO2. It was grown in RPMI1640 culture medium, and supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher Scientific, Waltham, MA, USA) and 1% penicillin and streptomycin. All cell stocks were authenticated at the USC Norris Cancer Center cell culture facility by comparison to the ATCC and/or published genomic criteria for that specific cell line; all cells were documented as free of mycoplasma. In situ Hi-C was performed in duplicate and 5 x 10^6 cells were used for each experiment. MboI restriction enzyme (NEB, R0147) was used to digest chromatin. For ligation, T4 DNA Ligase (NEB, M0202) was added and incubated at room temperature for 4 hours with slow rotation. Hi-C material was sheared to a size of 300-500bp using a Covaris instrument (Covaris S2, Woburn, MA). Biotin-tagged DNA was pulled down using Dynabeads MyOne Streptavidin C1 beads (Life technologies, 65002) with 2X Binding Buffer (2X BB: 10mM Tris-HCl (pH 7.5), 1nM EDTA, 2M NaCl). In situ Hi-C ibraries were prepared using Kapa Hyper prep kit (Kapa #KK8503) according to the provided protocol. Library was amplified with PCR and then sequenced using Illumina HiSeq 2000.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We performed Hi-C, Micro-C, and capture Micro-C  in human prostate cancer cells and compared chromatin interactions called using different methods. By integrating Micro-C with NOMe-seq, ChIP-seq, and RNA-seq, we investigated the relationships among nucleosome positioning of regulatory elements, chromatin interactions, and transcription. This work provides a framework for understanding the chromatin interactions among regulatory elements, nucleosome-depleted regions, and transcription. Overall design: Hi-C in C42B prostate cancer cells
SAMPLE_TITLE: C42B, HiC, rep2
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "C42B"}, {"TAG": "cell line", "VALUE": "C42B"}, {"TAG": "cell type", "VALUE": "Human prostate cancer cells"}]
Pool_Member_@attributes_sample_title: C42B, HiC, rep2
RUN_SET_RUN_Pool_Member_@attributes_sample_title: C42B, HiC, rep2
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "C42B_HiC_rep2_R1.fastq", "size": "63991484921", "date": "2022-05-27 15:20:40", "md5": "37351ed22ec1dbd248c39087a9568784", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "C42B_HiC_rep2_R2.fastq", "size": "63991484921", "date": "2022-05-27 15:15:49", "md5": "2ffb0686b2b3de77a54f9dce0475bd7d", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR19430921", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR19430921/SRR19430921", "size": "17267444102", "date": "2022-05-27 15:26:31", "md5": "ce010686c41cb338a7b9a160516b3429", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR19430921.lite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos2/sra-pub-zq-18/SRR019/19430/SRR19430921/SRR19430921.lite.1", "size": "11491045394", "date": "2022-10-15 21:18:14", "md5": "e71e8dec833bf25eefc2de25d2e82713", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]