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Sample GSM837613 Query DataSets for GSM837613
Status Public on Jan 03, 2012
Title lenti-DUX4-fl
Sample type SRA
Source name lenti-DUX4-fl
Organism Homo sapiens
Characteristics chip antibody: Combined anti-DUX4 C-terminus rabbit polyclonal antibodies MO488 and MO489
treatment: myoblasts transduced with lentivirus carrying DUX4
cell type: human myoblasts
Growth protocol Primary myoblasts grown in F-10 nutrient media, 20% FBS, 1% Pen/Strep, 10 ng/ml bFGF and 1 µM Dexamethasone. 
Extracted molecule genomic DNA
Extraction protocol Standard Illumina ChIP-seq sample prep kit protocol with two modifications: (1) DNA fragments ranging from 150 to 300 bp were selected at the gel-selection step; (2) 21 cycles of PCR were performed at the PCR amplification step instead of 18.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer IIx
Data processing Sequence reads were obtained using the Illumina Genome Analyzer IIx. Reads were aligned to human genome (hg18) using BWA. Peaks are called using in-house developed R package peakSig.
Submission date Nov 21, 2011
Last update date May 15, 2019
Contact name Stephen Tapscott
Organization name Fred Hutch Cancer Research Center
Department Human Biology
Lab Tapscott
Street address 1100 Fairview N. Ave
City Seattle
State/province WASHINGTON
ZIP/Postal code 98103
Country USA
Platform ID GPL10999
Series (1)
GSE33838 DUX4 activates germline genes, retroelements and immune-mediators: Implications for facioscapulohumeral dystrophy
SRA SRX107284
BioSample SAMN00760375

Supplementary file Size Download File type/resource
GSM837613_Dux4.full.peak.bedGraph.gz 602.2 Kb (ftp)(http) BEDGRAPH
GSM837613_Dux4.full.peak.csv.gz 835.0 Kb (ftp)(http) CSV
GSM837613_Dux4_full_rep1_sorted.bai.gz 2.1 Mb (ftp)(http) BAI
GSM837613_Dux4_full_rep1_sorted.bam 1.4 Gb (ftp)(http) BAM
GSM837613_Dux4_full_rep2_sorted.bai.gz 2.0 Mb (ftp)(http) BAI
GSM837613_Dux4_full_rep2_sorted.bam 1.1 Gb (ftp)(http) BAM
GSM837613_Dux4_full_rep3_sorted.bai.gz 1.8 Mb (ftp)(http) BAI
GSM837613_Dux4_full_rep3_sorted.bam 996.2 Mb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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