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| Status |
Public on Feb 19, 2020 |
| Title |
O(-Ex) replicate 3 |
| Sample type |
SRA |
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| Source name |
Skeletal muscle stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C56BL/6
gender: male
age: 18 months
activity: No Exercise
ccnd1: WT
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
FACS-isolated MuSCs were snap-frozen. RNA was extracted using the Nucleospin RNA XS kit (Machery-Nagel)
RNA (10 ng) was reverse-transcribed using oligo(dT) priming with the SMARTer Ultra Low Input system (Takara). The cDNA was then sheared with a Covaris S2 ultrasonicator. End repair, multiplexed adaptor ligation, and 13-15 cycles of library amplification were performed using the Ovation Ultralow Multiplex system (NuGEN). Libraries underwent paired-end 101-bp sequencing at the Stanford Genome Sequencing Service Center with an Illumina HiSeq 2000 to a depth of 20-40 million reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Reads were adapter- and quality-trimmed with trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore) (quality cutoff 20, adaptor stringency 1, final length filter 50). Trimmed reads were mapped to mm10 (Ensembl release 89, no patches) using transcript annotations from GENCODE with STAR (Dobin et al. 2013) (mismatch cutoff 4% of read length, no non-canonical junction alignments). Exonic reads that mapped uniquely were summarized over genes with the featureCounts module of the Subread package (Liao et al. 2014).
Genes lacking an Entrez ID or lacking a raw FPKM value of at least 1.5 in at least 3 samples were filtered out, resulting in ~11,000 genes. Raw count data were then normalized for library preparation and sample collection batch effects using RUVs (Risso et al. 2014) (k=6).
Ccnd1 Pearson correlation coefficients were calculated using log-transformed post-normalization FPKM values, using the weights package in R. To give each replicate group equal contribution to the correlation coefficient, sample weights were assigned to be 1/(group size).
Supplementary_files_format_and_content. Tab-delimited .txt file containing normalized FPKMs and Ccnd1 correlation coefficients for each gene
Genome_build: mm10
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| Submission date |
Jan 25, 2016 |
| Last update date |
Feb 19, 2020 |
| Contact name |
Jamie O. Brett |
| E-mail(s) |
jamie.o.brett@gmail.com
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| Organization name |
Stanford University
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| Department |
Neurology and Neurological Sciences
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| Lab |
Thomas A. Rando
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| Street address |
3801 Miranda Avenue, Building 100, Room E4-216
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| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE77178 |
Transcriptional profiles of skeletal muscle stem cells from mice of different ages, exercise status, and Ccnd1 genotypes |
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| Relations |
| BioSample |
SAMN04437884 |
| SRA |
SRX1543424 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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