|
| Status |
Public on Sep 05, 2013 |
| Title |
p53 ChIP |
| Sample type |
SRA |
| |
|
| Source name |
E15.5 WT kidney
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL
genotype/variation: wild type
age: E15.5
chip antibody: anti-p53 antibody (Santa Cruz Biotech; catalog# sc-6243; lot# C1609)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted from formaldehyde-crosslinked cells and ChIP-ed using anti-p53 antibody sc-6243 (Santa Cruz Biotech; lot# C1609).
ChIP DNA was processed into library by following the Illumina ChIP-Seq library construction protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
ChIP against p53
|
| Data processing |
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Alignment: Reads were aligned to human genome mm9 using Eland software (Illumina pipeline).
Peaks: MACS peak calling algorithm was used with a cut-off of pvalue = 1.00e-06 (http://liulab.dfci.harvard.edu/MACS/).
Genome_build: mm9
Supplementary_files_format_and_content: bed reports MACS peaks
|
| |
|
| Submission date |
Aug 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuwen Li |
| Organization name |
Tulane University
|
| Department |
Pediatrics
|
| Lab |
Pediatric Nephrology
|
| Street address |
1430 Tulane Ave SL37 RM5534
|
| City |
New Orleans |
| ZIP/Postal code |
70112 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE49916 |
Genome-wide analysis of p53 binding by ChIP-seq |
|
| Relations |
| BioSample |
SAMN02318155 |
| SRA |
SRX335560 |
