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Sample GSM1226520 Query DataSets for GSM1226520
Status Public on Oct 28, 2013
Title UNG KO gammaH2AX ChIP-seq, pemetrexed-treated
Sample type SRA
 
Source name Cultured cells
Organism Homo sapiens
Characteristics cell line: DLD1
genotype/variation: UNG knockout; UNG-/-
treated with: pemetrexed
chip antibody: Anti-gamma H2A.X (phospho S139) antibody
chip antibody vendor: Abcam
chip antibody cat. #: ab2893
Extracted molecule genomic DNA
Extraction protocol ChIP was performed as described (PMID 19275939).
Sequencing libraries were constructed as described (PMID 19275939) with the exception of the library amplification step. Instead of Phusion DNA polymerase, Expand High Fidelity PLUS (Roche) was used with the following cycling parameters: The following parameters were used for thermal cycling: 5 min at 94°C, 18 cycles of 30 sec at 94°C, 30 sec at 65°C, and 60 sec at 72°C followed by a 7 min final elongation at 72°C.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiScanSQ
 
Data processing Unique reads were aligned to the hg18 genome assembly using Bowtie, discarding reads with > 1 reportable alignment (-m 1)
Peaks were called using MACS 1.4 using the drug-treated sample as the treatment file and the untreated sample as the control file with a step size of 25 bp
Genome_build: hg18
Supplementary_files_format_and_content: sgr files were created from MACS-generated wig files and give ChIP-seq signal in 25 bp windows across chromosomes 1-22 and X
 
Submission date Sep 09, 2013
Last update date May 15, 2019
Contact name Peter Scacheri
E-mail(s) pxs183@case.edu
Organization name Case Western Reserve University
Department Genetics and Genome Sciences
Street address 2109 Adelbert Rd.
City Cleveland
State/province OH
ZIP/Postal code 44106
Country USA
 
Platform ID GPL15456
Series (1)
GSE50692 Uracil DNA glycosylase (UNG) loss enhances DNA double strand break formation in human cancer cells exposed to pemetrexed
Relations
BioSample SAMN02351232
SRA SRX347196

Supplementary file Size Download File type/resource
GSM1226520_UNG_KO_pemetrexed_yH2AX.sgr.tar.gz 313.1 Mb (ftp)(http) TAR
GSM1226520_UNG_KO_pemetrexed_yH2AX_peaks.txt.gz 45.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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