|
| Status |
Public on Feb 22, 2017 |
| Title |
15_1_Basal |
| Sample type |
SRA |
| |
|
| Source name |
Muscle biopsy before exercise
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Skeletal Muscle
treatment: control
time: Basal
individual: 15
|
| Treatment protocol |
Skeletal muscle biopsies collected from danish male subjects (age 22.6+/- 0.52, body mas index 23.08+/-0.87) at fasting conditions at rest and four hours after completion of a 15-minute exercise bout. Biopsies were immediately snap-frozen in liquid nitrogen and stored at -80°C for further analyses.
|
| Growth protocol |
Human subjects were fasting at biopsy collection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were purified from skeletal muscle biopsies with the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) following manufacturer’s instructions. The quality of recovered RNA was assessed by using the Agilent RNA 6000 Nano Kit (Agilent Technologies). RNA concentration was determined by spectrophotometry with a NanoDrop 2000. After purification, RNA samples were stored at -80°C until further analysis
Libraries were prepared after ribosomal RNA depletion with the TruSeq Stranded Total Sample Prep Kit with Ribo-Zero Gold (Illumina). Sequencing was done on a HiSeq 2500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were trimmed for adapters and low quality flanking ends using Trim Galore v0.3.7 and Cutadapt v1.4.2 on default settings
Pre-processed reads were mapped to the human reference genome (hg19) with tophat2 using the “--b2-very-sensitive” setting
Gene coverages were computed with featureCounts and the Gencode v19 annotation
Differential expression was determined using edgeR v3.12.1 with the glmQLFit/glmQLFTest modeling framework
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file with differential expression statistics (genes along rows, stats along columns), tab delimited text file with gene read coverage (genes along rows, samples along columns)
|
| |
|
| Submission date |
Oct 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Lars Roed Ingerslev |
| E-mail(s) |
[email protected]
|
| Organization name |
Copenhagen University
|
| Department |
NNF Center for Basic Metabolic Research
|
| Lab |
Integrative Physiology
|
| Street address |
Blegdamsvej 3B
|
| City |
Copenhagen |
| ZIP/Postal code |
2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE87748 |
An electrical pulse stimulation protocol to study acute epigenetic response to muscle cell contraction uncovers acute hydroxymethylation of the exercise-responsive gene Nr4a3 [RNA-Seq] |
| GSE87749 |
An electrical pulse stimulation protocol to study acute epigenetic response to muscle cell contraction uncovers acute hydroxymethylation of the exercise-responsive gene Nr4a3 |
|
| Relations |
| BioSample |
SAMN05879244 |
| SRA |
SRX2229377 |
