|
| Status |
Public on Feb 01, 2017 |
| Title |
Sample_5_MMH6_WITHdox_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
cultured mouse myoblasts (C2C12)
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variarion: MMH6_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 |
Jan 05, 2017 |
| 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) |
| GSE87282 |
Conservation and innovation in the DUX4-family gene network |
| GSE93167 |
Conservation and innovation in the DUX4-family gene network [MMH6 RNA-Seq] |
|
| Relations |
| BioSample |
SAMN06205233 |
| SRA |
SRX2464258 |
