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Sample GSM3335732 Query DataSets for GSM3335732
Status Public on Sep 13, 2019
Title in situ Hi-C in 22Rv1 rep1
Sample type SRA
 
Source name Human prostate cancer cell line 22Rv1
Organism Homo sapiens
Characteristics cell line: 22Rv1
genotype: wild type
Growth protocol 22Rv1 cells (CRL-2505) were obtained from ATCC. Cells were cultured according to the suggested protocols at 37ÂșC with 5% CO2. The media RPMI 1640 supplemented with 10% fetal bovine serum (Gibco by Thermo Fisher, #10437036) plus 1% penicillin and 1% streptomycin was used to culture cells.
Extracted molecule genomic DNA
Extraction protocol In situ Hi-C experiments were performed in 22Rv1 cells following the original protocol by Rao et al with minor modifications. Hi-C was performed in duplicate and 5 x 106 cells were used for each experiment. 100U of MboI restriction enzyme (NEB, R0147) was used to digest chromatin. For ligation, 2000U 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).
Libraries were prepared using Kapa Hyper prep kit (Kapa #KK8503) according to the provided protocol. HiC library was amplified with 14 cycles of PCR using Illumina primers. Each library was sequenced with 75bp paired-end for ~500M read pairs using Illumina HiSeq 2000.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Data processing The quality of each Hi-C library was checked with FastQC and HICUP version 0.5.8. Raw fastq files were processed through the HiC-Pro version 2.8.0 to make the raw contact count matrices for multiple resolutions. The matrices were normalized using the iterative correction method (iced python library). Intra-chromosomal significant loops (50kb-10Mb range) were selected with the 5kb resolution contact count matrices using the Fit-Hi-C (false discovery rate (FDR) < 0.05). To increase the sequencing depth, two replicates were pooled and processed as above described.
Genome_build: GRCh37
Supplementary_files_format_and_content: *raw.matrix.txt files contain 3 columns of data: column 1 = region 1, column2 = region 2, column3 = contact frequency. *bed files include chromosome coordinates for each region. Count matrices are provided for 10kb or 40kb windows.
 
Submission date Aug 16, 2018
Last update date Sep 13, 2019
Contact name Suhn K Rhie
Organization name University of Southern California
Street address 1450 Biggy Street
City Los Angeles
State/province CA
ZIP/Postal code 90089
Country USA
 
Platform ID GPL11154
Series (1)
GSE118629 A prostate cancer chromatin interaction map
Relations
Reanalyzed by GSM3358191
BioSample SAMN09843418
SRA SRX4559657

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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