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Sample GSM2086313 Query DataSets for GSM2086313
Status Public on May 20, 2016
Sample type SRA
Source name cell line VCaP
Organism Homo sapiens
Characteristics shRNA: PRMT5 NTC
chip antibody: ERG
treatment: DHT
cell line: VCaP
Treatment protocol 24h ligand as indicated for each sample
Growth protocol DMEM, Charcol Dextran stripped FBS for hormone depletion(2days), Doxycycline for shRNA construct induction (5days)
Extracted molecule genomic DNA
Extraction protocol ChIP protocol - Purification using Magio beads
Kapa HTP library preparation kit on a Sciclone NGS workstation using MagBio beads
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description ChIP DNA
Data processing BWA version 0.7.4-r385, aln parameters -q 5 -l 32 -k 2 -t 4
MACS2 version, callpeak --SPMR -B -q 0.01 --keep-dup 1
cat , all AR ChIPseq summit files
bedtools v2.20.1 slop -b 200, all AR ChIPseq summit files
bedtools v2.20.1 merge -d 1 -c 4 union AR ChIPseq summit file
Qlucore Omics Explorerer 3.1(19) - Generating summary Matrix file using union AR ChIPseq Peakfile, counting reads falling withing Peak features, Normalization according to Omics Explorer
Genome_build: hg19
Supplementary_files_format_and_content: raw data, pass filter Illumina NextSeq500 fastq files. Summit files, bed format Macs2 output, ChIPseq summits
Submission date Mar 11, 2016
Last update date May 15, 2019
Contact name Thomas Westerling
Organization name Dana Farber Cancer institute
Department Medical Oncology
Lab Myles Brown
Street address 450 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platform ID GPL18573
Series (1)
GSE79128 AR and ERG ChIP-seq in presence or absence of PRMT5
BioSample SAMN04546538
SRA SRX1629255

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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