|
| 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 |
