|
| Status |
Public on Sep 06, 2022 |
| Title |
iMSBmal1-/- - 3 |
| Sample type |
SRA |
| |
|
| Source name |
Tibialis anterior muscle
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Skeletal muscle
treatment: Tamoxifen
strain: C57BL/6
genotype: HSA-MCM-Bmal1-/-
|
| Treatment protocol |
iMSBmal1fl/fl mice were treated with either 15% ethanol in sunflower seed oil or 2 mg day-1 tamoxifen via intraperitonial injections for five days to induce recombination.
|
| Growth protocol |
iMSBmal1fl/fl mice were maintained in 12L:12D conditions in a AAALAC approved facility until 12-16 weeks of age.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tibialis anterior muscles were isolated and flash frozen in liquid nitrogen. Muscles were pulverized under liquid nitrogen to prevent fiber type sampling bias then homogenized in Trizol before RNA was extracted with a Qiagen RNeasy kit using the standard protocol. RNA was treated with TURBO DNase (Ambion) to remove genomic DNA.
Libraries were prepared using KAPA Stranded RNAseq Kits with RiboErase according to standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
M17
|
| Data processing |
Sequenced reads were mapped using HISAT2 and gene counts were quantified using Htseq-count
Gene counts were quantified using HTseq-count
Differential gene expression was determined using DESeq2 using Cook's outliers to filter out low expression and alpha = 0.05 to for significance.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample.
Supplementary_files_format_and_content: Matrix table with DEseq2 counts for every gene and every sample.
|
| |
|
| Submission date |
Apr 14, 2021 |
| Last update date |
Sep 06, 2022 |
| Contact name |
Lance Riley |
| E-mail(s) |
lance.riley.91@gmail.com
|
| Organization name |
Vanderbilt University
|
| Department |
Biomedical Engineering
|
| Lab |
Merryman Mechanobiology Lab
|
| Street address |
9445 MRB4, 2213 Garland Ave
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE172067 |
The Skeletal Muscle Molecular Clock Regulates Sarcomere Length Through Titin Splicing [1] |
| GSE189865 |
The Skeletal Muscle Molecular Clock Regulates Sarcomere Length Through Titin Splicing |
|
| Relations |
| BioSample |
SAMN18741514 |
| SRA |
SRX10601274 |
