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Sample GSM2327777 Query DataSets for GSM2327777
Status Public on Mar 09, 2018
Title EWS502 NT BRCA1
Sample type SRA
 
Source name Ewing's sarcoma EWS502
Organism Homo sapiens
Characteristics cell line: EWS502
cell type: Ewing's sarcoma
treatment agent: DMSO (NT: No Treatment)
chip antibody: BRCA1 (Santa Cruz, Cat# sc-646)
Treatment protocol Samples were treated with either vehicle or indicated doses of etoposide for indicated amout of time before extraction of DNA.
Growth protocol Cells were grown in RPMI-40 supplemented with 10%FBS
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, fixed and sheared to an average length of 200-1500bp. 10% of the samples from each cell line were pooled to form the Input. RNAPII/BRCA1 antibody was used for immunoprecipitation. ChIP DNA was purified, sheared further to an average length of 350 bp and sequenced after library construction.
Sequencing library was prepared using standard Illumina protocols
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 3000
 
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 Sep 23, 2016
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 GPL21290
Series (2)
GSE68847 BRCA1, R-loops and Recombination defects in Ewing's sarcoma
GSE87324 BRCA1/RNApII regulation in Ewing's sarcoma (ChIP-seq)
Relations
BioSample SAMN05821221
SRA SRX2188678

Supplementary file Size Download File type/resource
GSM2327777_EWS502_cntl_BRCA1_ChIP_peaks.bed.gz 15.5 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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