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Sample GSM3240330 Query DataSets for GSM3240330
Status Public on May 13, 2021
Title ATAC-seq on A673 STAG2 null
Sample type SRA
 
Source name A673 clones with STAG2 null
Organism Homo sapiens
Characteristics cell line: A673 Ewing sarcoma
genotype/variation: STAG2 null
Growth protocol Cells were grown in suspension using RPMI 1640 with 15% FBS in T-75 flasks.
Extracted molecule genomic DNA
Extraction protocol Cells were harvested at a concentration of 500,000 cells/ml.
Illumina Nextera DNA Sample prep kit
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 3000
 
Data processing Basecalls performed using HiSeq 3000 Illumina. Quality control tests for unmapped sequences were performed based on the FastQC v.0.11.5 software (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequencing reads were aligned to the hg19 genome assembly using bwa v0.7.17 with the mem -M configuration.
Mapped chrM reads and duplicate reads were removed.
Peak calling was performed using the model-based MACS v1.4.3 software with the cut-off P ≤ 1e-05. The ENCODE black-listed regions for hg19 (available at https://www.encodeproject.org/annotations/ENCSR636HFF/) were removed from each set of peak regions.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Bigwig files for normalized coverage signal in units of reads per million mapped reads per bp (rpm/bp). Coverage was computed for bins of size 20 base pairs by using the bamCoverage module available in deepTools v2.5.3.
 
Submission date Jul 02, 2018
Last update date May 14, 2021
Contact name Gabriela Alexe
E-mail(s) galexe@broadinstitute.org
Organization name Broad Institute
Department Computational Biology and Bioinformatics
Street address 415 Main St.
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL21290
Series (2)
GSE116494 The effect of STAG2 loss in Ewing sarcoma [ATAC-Seq]
GSE116495 The effect of STAG2 loss in Ewing sarcoma
Relations
BioSample SAMN09532155
SRA SRX4330296

Supplementary file Size Download File type/resource
GSM3240330_A673.STAG2null.ATACseq.bw 166.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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