|
| Status |
Public on Aug 18, 2020 |
| Title |
muscly biopsy, overweight T2DM male, before cold acclimation, subject T03 |
| Sample type |
RNA |
| |
|
| Source name |
biopsy from the vastus lateralis muscle, taken from male overweight T2DM subject, before 10 day cold acclimation intervention period, subject T03
|
| Organism |
Homo sapiens |
| Characteristics |
subject id: T03
disease: type 2 diabete
time point: before 10 day cold acclimation intervention period
Sex: male
|
| Treatment protocol |
Subjects underwent a 10-day cold acclimation intervention. Prior to the cold acclimation, a muscle biopsy was taken from the vastus lateralis muscle following an overnight fast. During the 10-day cold acclimation protocol, subjects were exposed to an environmental temperature of 14–15 °C for 10 consecutive days: 2 h on day 1, 4 h on day 2, and 6 h on days 3 through 10. On day 10, after an overnight fast, a skeletal muscle biopsy was taken. See Hanssen et al. (Nat Med. 2015;21(8):863-5. doi: 10.1038/nm.3891, PMID: 26147760) for more details.
|
| Growth protocol |
Experimental procedures of the cold-acclimation study have been previously published (PMID: 26147760). In this study samples of seven overweight male individuals with type 2 diabetes (age 59 ± 6 years, BMI 29.9 ± 3.1 kg/m2; average ± SD) were included.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol and further purified using Rneasy columns. Samples were only included for further analyses in case of intact bands corresponding to 18S and 28S ribosomal subunits and absence of chromosomal peaks or RNA degradation products.
|
| Label |
biotin
|
| Label protocol |
Total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).
|
| |
|
| Hybridization protocol |
Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations (Affymetrix, Santa Clara, CA, USA).
|
| Scan protocol |
Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA, USA).
|
| Data processing |
Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.52.1).
|
| |
|
| Submission date |
Aug 14, 2020 |
| Last update date |
Aug 19, 2020 |
| Contact name |
Guido Hooiveld |
| E-mail(s) |
[email protected]
|
| Organization name |
Wageningen University
|
| Department |
Div. Human Nutrition & Health
|
| Lab |
Nutrition, Metabolism & Genomics Group
|
| Street address |
HELIX, Stippeneng 4
|
| City |
Wageningen |
| ZIP/Postal code |
NL-6708WE |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11532 |
| Series (2) |
| GSE156248 |
Comparative transcriptome analysis of human skeletal muscle in response to cold acclimation and exercise training in human volunteers. [A391] |
| GSE156249 |
Comparative transcriptome analysis of human skeletal muscle in response to cold acclimation and exercise training in human volunteers. |
|
