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Sample GSM4727588 Query DataSets for GSM4727588
Status Public on Aug 18, 2020
Title muscly biopsy, overweight T2DM male, before cold acclimation, subject T05
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 T05
Organism Homo sapiens
Characteristics subject id: T05
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.

Data table header descriptions
ID_REF
VALUE RMA signal (as log2)

Data table
ID_REF VALUE
7892501 1.169527461
7892502 2.215384726
7892503 1.155218505
7892504 6.139083045
7892505 1.565217842
7892506 2.307764782
7892507 1.429280884
7892508 4.373021523
7892509 8.970162306
7892510 3.166161369
7892511 1.020035554
7892512 3.85892344
7892513 1.405527892
7892514 5.832850553
7892515 5.961556929
7892516 0.69721588
7892517 2.506237869
7892518 0.994977688
7892519 2.289923622
7892520 6.821764951

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM4727588_G178_A7_T05-pre_9.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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