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Status |
Public on Sep 13, 2019 |
Title |
in situ Hi-C in 22Rv1 rep1 |
Sample type |
SRA |
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Source name |
Human prostate cancer cell line 22Rv1
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Organism |
Homo sapiens |
Characteristics |
cell line: 22Rv1 genotype: wild type
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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.
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Library strategy |
Hi-C |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
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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.
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Submission date |
Aug 16, 2018 |
Last update date |
Sep 13, 2019 |
Contact name |
Suhn K Rhie |
Organization name |
University of Southern California
|
Department |
Biochemistry and Molecular Medicine
|
Lab |
Rhie Lab
|
Street address |
1450 Biggy Street NRT 3504
|
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 |