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Sample GSM947410 Query DataSets for GSM947410
Status Public on Oct 16, 2012
Title PrEC Cells Input gDNA-seq
Sample type SRA
Source name PrEC
Organism Homo sapiens
Characteristics cell line: PrEC
Growth protocol Cells were grown at 37ºC with 5% CO2 in PREGM media (Cambrex).
Extracted molecule genomic DNA
Extraction protocol ~ 1 x 106 cells, in a 10cm dish, were fixed by adding formaldehyde at a final concentration of 1% and incubating for 10 minutes at 37°C. The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1mg/ml aprotinin and 1mg/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice. The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 basepairs. DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30ml H2O. The DNA was quantitated using Qubit and 10ng was used for Illumina library preparation using Illumina ChIP-Seq DNA Sample Prep Kit #IP-102-1001.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina Genome Analyzer IIx
Data processing Reads were mapped with bowtie 0.12.7 Only reads mapping uniquely to the genome were kept. Upto 3 mismatches to the reference sequence were allowed. When more than one read mapped to the same genomic position, only one read was kept at that position.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig. Counts across the whole genome in windows 20 bases wide, per 1 million mapped reads.
Submission date Jun 13, 2012
Last update date May 15, 2019
Contact name Aaron Statham
Organization name Garvan Institute of Medical Research
Department Cancer Department
Lab Epigenetics Research Laboratory
Street address 384 Victoria St
City Darlinghurst
State/province NSW
ZIP/Postal code 2010
Country Australia
Platform ID GPL10999
Series (2)
GSE38674 Genomic DNA in Normal and Cancerous Prostate Cells
GSE38685 Normal and Cancerous Prostate Cells
SRA SRX154486
BioSample SAMN01048169

Supplementary file Size Download File type/resource 441.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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