|
| Status |
Public on Apr 01, 2019 |
| Title |
Rest Phase_Sedentary_ZT16_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Gastrocnemius muscle
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57B6/J
tissue: Gastrocnemius muscle
age: 10-11-week-old
gender: Male
treatment: Sedentary
phase: Rest phase (ZT3)
zt: 16
|
| Treatment protocol |
At 10-11 weeks of age, the mice were divided into two different groups of exercise or sham-exercise treatment either during the early rest phase group (ZT3) or the early active phase group (ZT15). Exercised mice in the early rest phase group were subjected to a single-bout of acute exercise for 1 hour at ZT3, whereas exercised mice in the early active phase group were subjected to the exercise for 1 hour at ZT15. Sedentary control mice for corresponding exercised mice at the different daily times were placed on a stationary treadmill for 1 hour (sham-exercise). Mice were returned into their home cages and allowed free feeding and drinking after the exercise and sham-exercise treatment. At 0, 4, 8, 12,16 and 20 hours following exercise or sham-exercise treatment at each early rest and active phase, mice were sacrificed under isoflurane anesthesia and the gastrocnemius muscles were isolated. The tissues were immediately snap frozen in liquid nitrogen and stored at - 80oC for subsequent use.
|
| Growth protocol |
Mice were reared at 22±1oC with 12 hr light/dark cycle (light on at 6AM (ZT0) and light off at 6PM (ZT12)) and fed a standard rodent laboratory diet (#1310, Altromin, Germany) ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, #80224). RNA was checked for quality using the Bioanalyzer instrument (Agilent Technologies, Santa Clara, CA) and subject to the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina, San Diego, CA).
Libraries were subjected to 100-bp paired end sequencing on HiSeq 2500 (Illumina) at the Beijing Genomics Institute (BGI, Hong Kong).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Gene expression data from mouse seletal muscle at indicated ZT
|
| Data processing |
FastQC (v0.11.5) was applied for quality control.
RNA-seq reads were subjected to trimming of adapters and low quality flanking ends using Trim_Galore (v0.4.3 using Cutadapt v1.16).
Pre-processed reads were mapped to mm10 using STAR aligner (v2.5.3a) and gene coverages were computed with featureCounts (v1.5.2) and the Gencode annotation (GRCm38).
The list of RNAs was filtered for those with a read coverage larger than 2 CPM (counts per million) in at least 34 samples, and 11461 of the total 52636 annotated RNAs survived this inclusion criterion.
edgeR (v3.2.23) was used for examinning differential expression of replicated count data.
Genome_build: mm10
Supplementary_files_format_and_content: Text file in tab separated format with gene counts in units of count per million (CPM)
|
| |
|
| Submission date |
Feb 22, 2019 |
| Last update date |
Apr 02, 2019 |
| Contact name |
Shogo Sato |
| E-mail(s) |
shogo.sato@bio.tamu.edu
|
| Organization name |
Texas A&M University
|
| Department |
Biology
|
| Street address |
3258 TAMU, Biological Science Building West (BSBW) 309
|
| City |
College Station |
| State/province |
Texas |
| ZIP/Postal code |
77843-3258 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE126962 |
Circadian transcriptome in mouse skeletal muscle after exercise in the early rest versus active phase |
|
| Relations |
| BioSample |
SAMN10989667 |
| SRA |
SRX5411174 |
