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Sample GSM1340090 Query DataSets for GSM1340090
Status Public on Jul 06, 2014
Title DNAPKCS OHT HS ChipSeq technical replicate 1 and 2
Sample type SRA
 
Source name Cultured fibroblasts
Organism Homo sapiens
Characteristics genotype: normal foreskin
chip antibody: pDNA-PKcs (Abcam ab18192)
treatment: 300 nM 4-hydroxy tamoxifen (OHT) for 4 h
Treatment protocol Cells expressing the HA-tagged AsiSI:ER fusion protein were treated with 300 nM 4-hydroxy tamoxifen (OHT) or an equivalent amount of solvent (methanol) for 4 h to activate the AsiSI restriction enzyme.
Growth protocol The Hs68 strain of human foreskin fibroblasts (ATCC: CRL 1635) expressing an HA-tagged AsiSI:ER fusion protein were cultured in Dulbecco modified Eagles medium (DMEM) supplemented with 10% fetal calf serum (FCS), 100 IU/ml penicillin, and 100 μ/ml streptomycin.
Extracted molecule genomic DNA
Extraction protocol DNA samples were end repaired, poly-A tailed and Illumina single end adapters were ligated following the standard Illumina protocol with minor adjustments. Agencourt AMPure XP beads at 0.8x ratio were used to size select out adapter dimers after adapter ligation. The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix. Post PCR, AMPure XP beads were used at a 1:1 ratio to maintain size integrity and to allow use of the Invitrogen SizeSelect E-gel system. Samples were finally purified with QAIquick gel extraction kit and quality controlled on the DNA 1000 BioAnalyser 2100 chip before clustering and subsequent 50-51bp single end sequencing on the Illumina HiSeq 2500.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description Chip-Seq
Data processing Duplicates were removed using the Picard MarkDuplicates program (picard-tools package version 1.81; http://picard.sourceforge.net) with default parameters.
 
Submission date Mar 05, 2014
Last update date May 15, 2019
Contact name Gordon Peters
E-mail(s) gordon.peters@cancer.org.uk
Phone +44 207 269 3049
Organization name CRUK London Research Institute
Lab Molecular Oncology
Street address 44 Lincolns Inn Fields
City London
ZIP/Postal code WC2A 3LY
Country United Kingdom
 
Platform ID GPL16791
Series (1)
GSE55605 Role of Polycomb group proteins in the DNA damage response – a reassessment
Relations
BioSample SAMN02673415
SRA SRX481484

Supplementary file Size Download File type/resource
GSM1340090_DNAPKCS_OHT_HS_mergedTechReps_ChipSeq_genome.wig.gz 464.6 Mb (ftp)(http) WIG
GSM1340090_DNAPKCS_OHT_HS_mergedTechReps_ChipSeq_peaks.bed.gz 79.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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