|
| Status |
Public on Jul 06, 2014 |
| Title |
DNAPKCS METHANOL 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 solvent (methanol) 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 |
SAMN02673414 |
| SRA |
SRX481483 |
