|
Status |
Public on Mar 09, 2018 |
Title |
CHLA10 NT DRIP |
Sample type |
SRA |
|
|
Source name |
Ewing's sarcoma CHLA10
|
Organism |
Homo sapiens |
Characteristics |
cell type: Ewing's sarcoma cell line: CHLA10 growth protocol: Cells were grown in IMDM supplemented with 10%FBS transfection protocol: none treatment protocol: DMSO (NT: No Treatment) 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 |
SAMN03656576 |
SRA |
SRX1025898 |