|
| Status |
Public on Oct 23, 2013 |
| Title |
input LCL Doxo |
| Sample type |
SRA |
| |
|
| Source name |
lymphoblastoid cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Doxo treated lymphoblastoid cells
coriell id: GM12878
|
| Treatment protocol |
human lymphoblastoid cells were treated at a density of 900,000 cells/ml with 0.5 μM doxorubicin (Sigma) or water as a vehicle control for 18 hours
|
| Growth protocol |
human lymphoblastoid cells were grown as recommended by Coriell
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and p53-DNA complexes were isolated with mouse monoclonal anti-human p53 (BD Pharmingen, cat# 554294). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg18 genome assembly using Burrows-Wheeler Alignment (BWA) Tool with the default configurations
Uniquely mapped reads with mis-match <= 2 were used for peak detection
Peaks were called using QuEST (version 2.4) using the “Transcription factor binding site” setting (bandwidth of 30 bp, region size of 300 bp) and the “stringent peak calling” parameters (corresponding to 50-fold ChIP to input enrichment for seeding the regions, and 3-fold ChIP enrichment for extending the regions).
Peaks with FDR q <= 0.05
Genome_build: hg19
|
| |
|
| Submission date |
May 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Xuting Wang |
| E-mail(s) |
[email protected]
|
| Phone |
9842873840
|
| Organization name |
NIEHS/NIH
|
| Street address |
111 TW Alexander Dr
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE46991 |
Genome-wide map of p53 binding sites by ChIP-seq in human lymphoblastoid cell lines treated with doxorubicin |
|
| Relations |
| BioSample |
SAMN02144657 |
| SRA |
SRX278508 |
