|
| Status |
Public on Sep 26, 2016 |
| Title |
DINO_ChIRP_RNase_EVEN |
| Sample type |
SRA |
| |
|
| Source name |
U2OS osteosarcoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U2OS
cell type: U2OS osteosarcoma cell line
treated with: 0.2ug/mL doxorubicin for 24 hours
|
| Treatment protocol |
U2OS cells were treated with 0.2ug/mL doxorubicin for 24 hours prior to cell crosslinking with glutaraldehyde and chromatin fragmentation.
|
| Growth protocol |
p53 wildytpe U2OS cells were obtatined from ATCC and grown under standard culture condition.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Per ChIRPseq protocol. Chu C. et al. JoVE 2012.
Sequencing libraries were constructed using the NEB ChIPseq library preparation kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
library strategy: ChIRP-seq
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie. Peaks were called using the MACS2 narrow peak mode using the default parameters.
Number of Raw reads in each peak was calculated using in house generated script, and data matrix was normalized using R
Genome_build: hg19
Supplementary_files_format_and_content: ENCODE narrowPeak; Content: chrom, chromStart, chromEnd, name, score, strand, signalValue, pValue, qValue, peak
|
| |
|
| Submission date |
Dec 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Adam Schmitt |
| E-mail(s) |
amschmit@stanford.edu
|
| Phone |
650-736-0305
|
| Fax |
650-723-8762
|
| Organization name |
Stanford University
|
| Department |
Department of Dermatology
|
| Lab |
Howard Y. Chang
|
| Street address |
269 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5168 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE76418 |
lncRNA DINO ChIRPseq in DNA damaged U2OS cells |
| GSE76420 |
LncRNA DINO guides DNA damage signaling |
|
| Relations |
| BioSample |
SAMN04377115 |
| SRA |
SRX1508422 |
