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Sample GSM388918 Query DataSets for GSM388918
Status Public on Apr 03, 2009
Title Patient 4 Subcutaneous Lean
Sample type RNA
 
Source name adipose tissue
Organism Homo sapiens
Characteristics patient: 4
tissue: Subcutaneous adipose tissue
surgery: Hysterectomy
age: 53 years
gender: Female
body mass index: 24.2 BMI
body size category: lean
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 44.44108444
2 12.35628664
3 7.028969166
4 568.4955872
5 35.33028297
6 2.635584087
7 0.093405471
8 273.8064605
9 105.8775574
10 240.7376589
11 0.025471208
12 12.92887377
13 212.6496725
14 9.527616814
15 6.424739691
16 32.39054369
17 26.61081694
18 26.31022067
19 0.285915646
20 15.05804389

Total number of rows: 20469

Table truncated, full table size 344 Kbytes.




Supplementary file Size Download File type/resource
GSM388918.XLS.gz 1.4 Mb (ftp)(http) XLS
Processed data included within Sample table
Processed data provided as supplementary file

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