|
| Status |
Public on Mar 09, 2018 |
| Title |
U2OS-siEWSR1-2 Etop DRIP |
| Sample type |
SRA |
| |
|
| Source name |
Osteosarcoma U2OS
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Osteosarcoma
cell line: U2OS
growth protocol: Cells were grown in DMEM supplemented with 10%FBS
transfection protocol: Transfected with 40nmol of pooled siRNA against EWSR1 (ON-TARGETplus, Dharmacon, Cat#L-005119-02) using Lipofectamine RNAiMax (Invitrogen)
treatment protocol: 6μM Etoposide for 6 hours
drip antibody: S9.6 (Kerafast, Cat#ENH001)
|
| Treatment protocol |
Samples were treated with either vehicle (DMSO) or indicated doses of etoposide for indicated amout of time before extraction of RNA
|
| Growth protocol |
Cells were passaged in 10cm corningware dishes using media described in Samples section in a 37°C humidified incubator
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from sub-confluent dishes and fragment with HindIII, EcoRI, BsrGI, XbaI and SspI (NEB). Half the samples were further treated to RNASEH (NEB). 10% of the samples from each cell line were pooled to form the Input. Monoclonal antibody S9.6 that recognizes DNA:RNA hybrids was used to enrich for R-loops.
Sequencing library was prepared using standard Illumina protocols
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
library strategy: DRIP-seq
|
| Data processing |
Short reads were aligned to hg19 using BWA with default alignment parameters, and then post processed to limit to unique alignment and no more than 2 mis-match base-pairs
Peak calling by using MACS2 with parameters as follows: -g 2.7e9 -q 0.05 -B -m 3 30, and using corresponding Input as control sample
peaks (in bed file format) were further annotated to gene by using CEAS (v1.0.2)
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in bed format, which are the peak calling results by using MACS2.
|
| |
|
| Submission date |
May 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yidong Chen |
| E-mail(s) |
cheny8@uthscsa.edu
|
| Phone |
2105629163
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Population Health Sciences
|
| Street address |
8403 Floyd Curl Drive, MSC 7784
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE68845 |
BRCA1, R-loops and Recombination defects in Ewing's sarcoma (DRIP-seq) |
| GSE68847 |
BRCA1, R-loops and Recombination defects in Ewing's sarcoma |
|
| Relations |
| BioSample |
SAMN03656595 |
| SRA |
SRX1025913 |
