|
| Status |
Public on Jan 21, 2014 |
| Title |
siGATA2-AR_ChIP Seq |
| Sample type |
SRA |
| |
|
| Source name |
prostate cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: androgen-dependent prostate cancer derived cell line LNCaP
passage number: 32-34
chip antibody: AR [Santa cruz sc-816 (N-20) lot# D0513]
genotype/variation: siGATA2
|
| Treatment protocol |
LnCaP cells were treated with 40nM siControl or siGATA2 from Dharmacon company for 3 days. For AR ChIP, 1 nM R1881 was added before cell colllection for ChIP assay.
|
| Growth protocol |
LNCaP cells were cultured in 10% FBS RPMI 1640 medium, 1:2.5 split every 2 days. Cells are cultured in 5% charcoal stripped FBS rpmi 1640 medium
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and AR-DNA or FoxA1-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part#15023092 ). Briefly, DNA was end-repaired, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, the DNA was size selected from an agarose gel and was PCR amplified with Illumina primers for 15 cycles. Libraries were sequenced on the Hi-seq 2500 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 2
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.0.0 with parameters '-k 2 -v 2' to report up to two valid alignments
Read with multiple valid alignments were removed using a Perl program
Uniquely mapped reads from replicates of the same sample were pooled
Peaks were called using MACS v1.4.2 with parameters '-m 3,30 -g hs -p 1e-8'
Genome_build: hg19
Supplementary_files_format_and_content: wig
|
| |
|
| Submission date |
Nov 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Qianben Wang |
| E-mail(s) |
Qianben.Wang@osumc.edu
|
| Phone |
6142471609
|
| Organization name |
Ohio State University
|
| Department |
Molecular and Cellular Biochemistry and the Comprehensive Cancer Center
|
| Street address |
460 W 12th Avenue
|
| City |
Columbus |
| State/province |
Ohio |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE52725 |
Next Generation Sequencing Facilitates Quantitative Analysis of effect of knockdown of GATA2 on AR binding sites |
|
| Relations |
| BioSample |
SAMN02420425 |
| SRA |
SRX383816 |
