|
Status |
Public on Feb 01, 2017 |
Title |
Sample_C2C12_mDUX_36h_15B_NODOX2 |
Sample type |
SRA |
|
|
Source name |
cultured mouse myoblasts (C2C12)
|
Organism |
Mus musculus |
Characteristics |
genotype/variation: mDUX codon-altered treatment: NO 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.
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|
|
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.
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|
|
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 |
SAMN05806587 |
SRA |
SRX2187077 |