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Sample GSM625499 Query DataSets for GSM625499
Status Public on Aug 13, 2012
Title WAT_Nonobese [469_miRNA]
Sample type RNA
 
Source name Abdominal subcutaneous adipose tissue
Organism Homo sapiens
Characteristics tissue: White adipose tissue
gender: female
age: 41
Treatment protocol One part (400 mg) of the biopsy was kept at -70 °C for subsequent measures of miRNAs.
Growth protocol Subcutaneous adipose tissue biopsies (at least 1.5 g) was obtained from 56 subjects (30 obese and 26 non-obese) by needel aspiration and subsequently snap frozen in liquid nitrogen.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from snap frozen intact tissue and RNA concentration as well as purity was measured spectrophotometrically using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific) and high quality (total and small) RNA was confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
Label biotin
Label protocol 1 μg of total adipose RNA was labelled using the FlashTag biotin HSR labeling kit (Genisphere Inc., Hatfield, PA) according to the supplier’s protocol.
 
Hybridization protocol The labelled samples were placed in a hybridization cocktail mix containing 4% formamide and hybridised overnight to Affymetrix microRNA Arrays (Affymetrix Inc.) following the indicated Genisphere protocol.
Scan protocol The arrays were washed, stained and scanned in an Affymetrix GCS 3000 scanner.
Data processing Signal intensities and present calls were generated by using the microRNA QC tool by Affymetrix. The normalization algorithm used was the default settings in miRNA QCTool (from Affymetrix), that is background adjustment, BC-CG Adjust; normalization, Quantile; summarization, median polish.
 
Submission date Nov 18, 2010
Last update date Aug 14, 2012
Contact name Ingrid Dahlman
E-mail(s) ingrid.dahlman@ki.se
Organization name Karolinska
Street address Karolinska Huddinge
City Stockholm
ZIP/Postal code 14186
Country Sweden
 
Platform ID GPL8786
Series (2)
GSE25402 Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity
GSE25470 Adipose Tissue MicroRNAs as Regulators of CCL2 Production in Human Obesity [miRNA data]

Data table header descriptions
ID_REF
VALUE See "data processing", values are log2 transformed
DETECTION P-VALUE
DETECTION

Data table
ID_REF VALUE DETECTION P-VALUE DETECTION
AFFX-BioB-5_at 9.039964 1.88E-26 TRUE
AFFX-BioB-M_at 9.644855 2.88E-29 TRUE
AFFX-BioB-3_at 9.386861 2.42E-25 TRUE
AFFX-BioC-5_at 10.67813 1.61E-29 TRUE
AFFX-BioC-3_at 9.777843 1.22E-28 TRUE
AFFX-BioDn-5_at 11.6565 2.67E-30 TRUE
AFFX-BioDn-3_at 12.94282 3.07E-31 TRUE
AFFX-CreX-5_at 14.32203 9.75E-32 TRUE
AFFX-CreX-3_at 14.43027 1.48E-31 TRUE
AFFX-r2-Ec-c1-bioB-5_at 9.434677 9.00E-17 TRUE
AFFX-r2-Ec-c1-bioB-M_at 9.885519 2.18E-18 TRUE
AFFX-r2-Ec-c1-bioB-3_at 9.165619 2.20E-17 TRUE
AFFX-r2-Ec-c1-bioC-5_at 11.13823 1.28E-18 TRUE
AFFX-r2-Ec-c1-bioC-3_at 11.08396 2.76E-18 TRUE
AFFX-r2-Ec-c1-bioD-5_at 12.59123 1.28E-18 TRUE
AFFX-r2-Ec-c1-bioD-3_at 13.24232 1.02E-18 TRUE
AFFX-r2-P1-c1-cre-5_at 14.52932 1.40E-18 TRUE
AFFX-r2-P1-c1-cre-3_at 14.65777 1.20E-18 TRUE
AFFX-r2-Ec-c2-bioB-5_at 9.40559 9.00E-17 TRUE
AFFX-r2-Ec-c2-bioB-M_at 9.80491 1.20E-18 TRUE

Total number of rows: 7788

Table truncated, full table size 307 Kbytes.




Supplementary file Size Download File type/resource
GSM625499.CEL.gz 166.3 Kb (ftp)(http) CEL
Processed data included within Sample table

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