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Sample GSM2326662 Query DataSets for GSM2326662
Status Public on Feb 01, 2017
Title Sample_C2C12_mDUX_36h_15B_DOX1
Sample type SRA
Source name cultured mouse myoblasts (C2C12)
Organism Mus musculus
Characteristics genotype/variation: mDUX codon-altered
treatment: DOXYCYCLINE
Treatment protocol 2ug/ml doxycycline treatment for 36 hours
Growth protocol C2C12, mouse myoblasts (ATCC® CRL-1772™), were grown in DMEM (Gibco/Life Technologies) supplemented with 10% fetal bovine serum (Thermo Scientific) and 1% penicillin/streptomycin (Life Technologies) and 2.6ug/ml puromycin to select for cells carrying the transgene indicated.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from whole cells using NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer's instructions.
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone NGSx Workstation (PerkinElmer, Waltham, MA, USA).
RNA-seq libraries were pooled (14-plex) and clustered onto two flow cell lanes.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Data processing Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Removed reads with at least one "N" in the sequence from the raw FASTQ files.
Aligned FASTQ files using tophat-2.0.12 and bowtie2-2.2.3.
Counted gene hits using Bioconductor's summerizeOverlaps() function with "Intersection-Strict" mode.
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts in CSV format annotated by UCSC known gene track on mm10.
Submission date Sep 22, 2016
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 GPL17021
Series (2)
GSE87266 Conservation and innovation in the DUX4-family gene network (RNA-seq)
GSE87282 Conservation and innovation in the DUX4-family gene network
BioSample SAMN05806591
SRA SRX2187073

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data included within Sample table

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