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Sample GSM2326657 Query DataSets for GSM2326657
Status Public on Feb 01, 2017
Title Sample_C2C12_Luc2A_36h_DOX2
Sample type SRA
 
Source name cultured mouse myoblasts (C2C12)
Organism Mus musculus
Characteristics genotype/variation: Luciferase
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
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 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
Relations
BioSample SAMN05806596
SRA SRX2187068

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

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