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Sample GSM1600544 Query DataSets for GSM1600544
Status Public on Feb 04, 2015
Title GATA2_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: 32-35
cell type: androgen dependent
chip antibody: GATA2 santa cruz sc-9008(H116) lot# E0313
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 genomic DNA
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 Feb 03, 2015
Last update date May 15, 2019
Contact name Qianben Wang
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
BioSample SAMN03328458
SRA SRX864826
Named Annotation GSM1600544_LNCaP_GATA2.wig.gz

Supplementary file Size Download File type/resource
GSM1600544_LNCaP_GATA2.wig.gz 456.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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