|
| Status |
Public on Jul 13, 2021 |
| Title |
3940_0h_IP |
| Sample type |
SRA |
| |
|
| Source name |
mouse sarcoma
|
| Organism |
Mus musculus |
| Characteristics |
cell type: mouse sarcoma
cell line: 3940
treatment: untreated
chip antibody: p53 antibody (NCL-L-p53-CM5p, Leica Biosystems)
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 |
SAMN17103412 |
| SRA |
SRX9697342 |
