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Sample GSM2267343 Query DataSets for GSM2267343
Status Public on Sep 21, 2016
Title Sample_6-MB135_HDUX4CA_WITHdox_rep3
Sample type SRA
 
Source name Cultured myoblasts
Organism Homo sapiens
Characteristics cell type: Facioscapulohumeral dystrophy (FSHD)
tissue: Immortalized primary myoblasts
treatment: Doxycyline
Extracted molecule polyA RNA
Extraction protocol RNA was extracted from myoblasts using TRIzol reagent as per manufacturer's instructions and cleaned up using Qiagen Rneasy columns, including the optional, on-column DNAse digestion step.
The Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Samples were multiplexed using Illumina barcodes to run 2-6 samples per sequencing lane.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Data processing Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Reads were mapped to the hg19 human genome assembly using Bowtie v1.0.0 and RSEM v1.2.4. RSEM was modified to call Bowtie with the -v 2 mapping strategy. RSEM was then invoked with the arguments --bowtie-m 100 --bowtie-chunkmbs 500 --calc-ci --output-genome- bam on the gene annotation file.
Sample 1 to 6 are used to generate the processed csv files with EdgeR-based expression estimates and fold change values (with dox vs withoutdox) for coding genes.
Genome_build: hg19
 
Submission date Aug 11, 2016
Last update date May 15, 2019
Contact name Stephen Tapscott
E-mail(s) stapscot@fredhutch.org
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 GPL18460
Series (1)
GSE85461 Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells
Relations
BioSample SAMN05559942
SRA SRX2012537

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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