|
| Status |
Public on Feb 09, 2017 |
| Title |
Skeletal Muscle Sample 29_vibration, control |
| Sample type |
RNA |
| |
|
| Source name |
skeletal muscle, vibration, control
|
| Organism |
Homo sapiens |
| Characteristics |
stress: vibration
tissue: soleus muscle
gender: male
|
| Treatment protocol |
Subjects completed a single session of active muscle contractions using neuromuscular electrical stimulation, passive limb-vibration, or systemic heat stress three hours before a muscle biopsy. Each subject's opposite limb was used as a within subject control for gene expression analaysis.
|
| Growth protocol |
Not Applicable
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following harvest, muscle biopsy samples were immediately placed In RNALater (Ambion) and stored at -80 C until further use. Total RNA was extracted using TRIzol solution (Invitrogen) according to the manufacturer’s instructions. 50 ng of RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN MinElute Reaction Cleanup column (QIAGEN Cat #28204) according to modifications from NuGEN. Four μg of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.
|
| Label |
Biotin
|
| Label protocol |
5μg of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.
|
| |
|
| Hybridization protocol |
Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer and placed onto Affymetrix Human Exon 1.0 ST arrays. Hybridizations were performed by the Iowa Institute of Human Genomics (IIHG) at the University of Iowa.
|
| Scan protocol |
Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the GeneChip operating software (GCOS) v1.4.
|
| Data processing |
Arrays were normalized using a GC-Robust Multi-array Average (GC-RMA) and transformed into a log2 hybridization signal using Partek Genomic Suites (v6.6 Copyright © 2013 Partek Inc., St. Louis, MO, USA).
|
| |
|
| Submission date |
Jun 07, 2016 |
| Last update date |
Feb 09, 2017 |
| Contact name |
Richard Shields |
| Organization name |
The University of Iowa
|
| Street address |
1-252 Medical Education Building
|
| City |
Iowa City |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (1) |
| GSE82323 |
Distinct skeletal muscle gene regulation from active contraction, passive vibration, and whole body heat stress in humans |
|
