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Sample GSM602093 Query DataSets for GSM602093
Status Public on Sep 30, 2011
Title Subject 11 after LCD
Sample type RNA
 
Channel 1
Source name after LCD
Organism Homo sapiens
Characteristics source material: study participant, subcutaneous adipose tissue, periumbilical area
weight class: weight regainer
time: after LCD
Treatment protocol Subcutaneous adipose tissue samples from the periumbilical area were obtained by needle aspiration under local anaesthesia after an overnight fast at each of the time points. Biopsy samples were stored at -80°C until analysis.
Growth protocol 8 week low calorie diet (LCD; 3.3 MJ/d; 800 kcal).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy total RNA Mini kit (Qiagen).
Label Cy5
Label protocol According to Agilent instructions. RNA from study participant labeled with Cy5, RNA from reference pool labeled with Cy3.
 
Channel 2
Source name reference RNA
Organism Homo sapiens
Characteristics source material: commercial pool of human liver, heart, intestine tissue, skeletal muscle RNA
Treatment protocol Subcutaneous adipose tissue samples from the periumbilical area were obtained by needle aspiration under local anaesthesia after an overnight fast at each of the time points. Biopsy samples were stored at -80°C until analysis.
Growth protocol 8 week low calorie diet (LCD; 3.3 MJ/d; 800 kcal).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy total RNA Mini kit (Qiagen).
Label Cy3
Label protocol According to Agilent instructions. RNA from study participant labeled with Cy5, RNA from reference pool labeled with Cy3.
 
 
Hybridization protocol Sample preparation, hybridization, and microarray washing were performed according to manufacturer’s instructions (Agilent Technologies).
Scan protocol Scanned using a GenePix 4000A Scanner (Axon Instruments-Molecular Devices).
Description Subject 11 after LCD
Data processing Microarray normalization was carried out by subtracting the median intensity background signal prior to intra-slide Loess normalization of log-transformed data (Goulphar Version 1.1.3 package). All data was then uploaded into the JMP Genomics Version 4.1 platform and further normalized using a quantile inter-slide intensity method.
 
Submission date Sep 29, 2010
Last update date May 04, 2012
Contact name David M Mutch
E-mail(s) dmutch@uoguelph.ca
Phone +1-519-824-4120
Organization name University of Guelph
Department Human Health & Nutritional Sciences
Lab ANNU 308
Street address 50 Stone Road East
City Guelph
State/province Ontario
ZIP/Postal code N1G 2W1
Country Canada
 
Platform ID GPL4133
Series (1)
GSE24432 Subcutaneous adipose tissue: comparison of weight maintainence and weight regain following an 8-week low calorie diet

Data table header descriptions
ID_REF
VALUE Loess normalized log-transformed data (participant/reference)

Data table
ID_REF VALUE
1 -0.661
2 -0.101
3 -0.147
4 -0.362
5 -0.304
6 0.057
7 -0.339
8 -0.261
9 0.248
10 0.198
11 0.137
12 0.525
13 0.173
14 0.123
15 -0.08
16 -0.46
17 0.488
18 -0.191
19 1.103
20 0.073

Total number of rows: 45220

Table truncated, full table size 535 Kbytes.




Supplementary file Size Download File type/resource
GSM602093.gpr.gz 6.2 Mb (ftp)(http) GPR
Processed data included within Sample table

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