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Sample GSM1683492 Query DataSets for GSM1683492
Status Public on Mar 09, 2018
Title CHLA10 Etop 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: 0.15μM 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 SAMN03656577
SRA SRX1025899

Supplementary file Size Download File type/resource
GSM1683492_CHLA10_Etop_vs_Input_peaks.bed.gz 415.9 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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