|
Status |
Public on Jul 13, 2021 |
Title |
3472_24h_input |
Sample type |
SRA |
|
|
Source name |
mouse sarcoma
|
Organism |
Mus musculus |
Characteristics |
cell type: mouse sarcoma cell line: 3472 treatment: 500 nM 4-hydroxytamoxifen for 24h chip antibody: none experimental series: p53 reconstitution ChIP
|
Treatment protocol |
Cells were harvested untreated or 24 hours post treatment with 500 nM 4-hydroxytamoxifen (4-OHT)
|
Growth protocol |
Cell lines were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco), 0.1 mM nonessential amino acids, 2 mM L-glutamine, and Pen/Strep (50 U/ml).
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Lysates were clarified from sonicated nuclei and bound DNA fragments were isolated with p53 antibody (NCL-L-p53-CM5p, Leica Biosystems). Genomic DNA libraries were prepared for sequencing using standard Illumina protocols.
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 4000 |
|
|
Data processing |
Reads were aligned to the mouse genome (genome build mm10) with Bowtie version 1.0.1 allowing up to 2 mismatches. For reads with multiple reportable alignments, one was reported at random (-M 1) Peaks were called with Macs2 2.2.7.1 Genome_build: mm10 Supplementary_files_format_and_content: BED files for peaks were generated using MACS 2.2.7.1. Processed data is the unmodified narrow peak output.
|
|
|
Submission date |
Dec 17, 2020 |
Last update date |
Jul 13, 2021 |
Contact name |
Jesse R Zamudio |
E-mail(s) |
jesse.zamudio@ucla.edu
|
Organization name |
University of California, Los Angeles
|
Department |
MCDB
|
Lab |
Zamudio
|
Street address |
610 CHARLES E. YOUNG DRIVE EAST BOX 957239
|
City |
LOS ANGELES |
State/province |
CA |
ZIP/Postal code |
90095-7239 |
Country |
USA |
|
|
Platform ID |
GPL21103 |
Series (2) |
GSE163402 |
The p53 transcriptional response across tumor types reveals core and outcome-specific signatures modulated by cis-regulatory lncRNAs [ChIP-seq] |
GSE163404 |
The p53 transcriptional response across tumor types reveals core and outcome-specific signatures modulated by cis-regulatory lncRNAs |
|
Relations |
BioSample |
SAMN17103401 |
SRA |
SRX9697335 |