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Sample GSM388911 Query DataSets for GSM388911
Status Public on Apr 03, 2009
Title Patient 19 Omental Obese
Sample type RNA
 
Source name adipose tissue
Organism Homo sapiens
Characteristics patient: 19
tissue: Omental adipose tissue
surgery: Gastric bypass
age: 45 years
gender: Female
body mass index: 62 BMI
body size category: obese
Extracted molecule total RNA
Extraction protocol Adipose tissue was collected at the beginning of the operation (within 30 minutes) into sterile 50 mL conical tubes and immediately flash- frozen in liquid nitrogen. Subcutaneous adipose tissue was collected from the subcutaneous abdominal wall and omental adipose tissue was collected from the greater omentum which is representative of intra-abdominal adipose depots drained by the portal vein. RNA was extracted from tissues using Qiagen spin columns (Qiagen, Mississauga, Canada) following manufacturer’s protocol for fatty tissue with the addition of two RNase free DNase treatments (Qiagen) between RW1 washes. RNA quality was assessed by spectrometry (260/280 ratio) with ratios of 1.9 – 2.0. As well, RNA quality was assessed by chromatography.
Label Biotin labelled cRNA
Label protocol cRNA was synthesized by in vitro transcription and hybridisation as previously described. Briefly, 10 ug of high quality total RNA was converted to cDNA and then to biotin-labelled cRNA (10 mM Biotin-11-UTP, Perkin-Elmer) by linear amplification (iExpress Assay reagent kit, GE Healthcare Bio-Sciences, Montreal, Quebec).
 
Hybridization protocol 10 ug of labelled cRNA was hybridised to CodeLink UniSet Human 20K I (GE Healthcare Bio-Sciences).
Scan protocol The microarray slides were processed according to manufacturer’s instructions and analysed using Codelink System Software (GE Healthcare Bio-Sciences).
Description 10 ug of labelled cRNA was hybridised to CodeLink UniSet Human 20K I (GE Healthcare Bio-Sciences). The microarray slides were processed according to manufacturer’s instructions and analysed using Codelink System Software (GE Healthcare Bio-Sciences). The spot intensities were median normalized (signal intensity of probe / median intensity of all discovery probes).
Data processing The spot intensities were median normalized (signal intensity of probe / median intensity of all discovery probes).
 
Submission date Apr 02, 2009
Last update date Apr 19, 2010
Contact name Katherine Cianflone
E-mail(s) katherine.cianflone@crhl.ulaval.ca
Organization name Laval University
Street address 2725 Ste Foy
City Quebec
State/province Quebec
ZIP/Postal code G1V 4G5
Country Canada
 
Platform ID GPL4044
Series (1)
GSE15524 Individualized analysis of subcutaneous and omental abdominal adipose tissue from non-obese and obese subjects

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
1 55.21721547
2 4.451881532
3 0.597662167
4 1775.69838
5 27.98916872
6 0.365126935
7 0.332545404
8 833.5467219
9 82.95906293
10 171.8915118
11 0.505714074
12 3.182634057
13 157.7889034
14 27.51213404
15 20.89105525
16 30.38682662
17 138.8696113
18 30.2775808
19 0.151714222
20 13.71489202

Total number of rows: 20469

Table truncated, full table size 345 Kbytes.




Supplementary file Size Download File type/resource
GSM388911.XLS.gz 1.4 Mb (ftp)(http) XLS
Processed data included within Sample table
Processed data provided as supplementary file

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