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Sample GSM105991 Query DataSets for GSM105991
Status Public on Apr 28, 2006
Title High weight gainer Kozak1_ABI_ING_H3
Sample type RNA
 
Source name inguinal fat
Organism Mus musculus
Characteristics mouse adipose tissue
Extracted molecule total RNA
Extraction protocol Tissues were quickly removed and frozen in liquid nitrogen and stored at -80C for subsequent preparation of total RNA. Total RNA was isolated using TRI-Reagent (Molecular Research Center Inc. Cincinnati, Ohio) with modifications to remove DNA using the Qiagen RNAeasy columns and DNaseI Kit (Qiagen, Valencia, CA). RNA was stored at –70C in RNase-free H2O supplemented with the RNase inhibitor Superasin (Ambion, Austin, TX) as per manufacturers directions. Quality and quantity of RNA was determined using a Agilent Bioanalyzer as per manufacturers procedures (Agilent Technologies, Palo Alto, CA).
Label DIG-UTP
Label protocol 1 ug of total RNA was used to transcribe DIG-labeled cRNA using Applied Biosystems Chemiluminescent RT-IVT Kit V2.0.
 
Hybridization protocol Microarray hybridization (using twenty micrograms of fragmented, DIG-labeled cRNA) and processing were performed according to Applied Biosystems protocols.
Scan protocol Chemiluminescence detection, imaging, auto gridding, and image analysis was done according to Applied Biosystems protocols and the 1700 Chemiluminescent Microarray Analyzer Software v. 1.0.3.
Description Pooled inguinal fat from 8 C57BL/6J mice with 'high' weight gain after 4 weeks on a high fat diet (D12331;Research Diets, New Brunswick, NJ). Microarrays were performed in triplicate, H1, H2 and H3.
Data processing Signal intensities across microarrays were normalized using the quantile-quantile method (www.bioconductor.org).
 
Submission date Apr 20, 2006
Last update date Sep 25, 2006
Contact name Robert A. Koza
E-mail(s) kozara@pbrc.edu
Phone 225-763-3191
Organization name Pennington Biomedical Research Center
Department Genomics Core Facility
Street address
City Baton Rouge
State/province LA
ZIP/Postal code 70808
Country USA
 
Platform ID GPL2995
Series (1)
GSE4692 Diet-induced obesity Kozak1_ABI_ING

Data table header descriptions
ID_REF
VALUE same as UNF_VALUE but with flagged values removed
SIGNAL_RAW raw signal intensity
STDEV noise/background signal intensity
S2N signal to noise ratio is equal to SIGNAL_RAW/STDEV
CV Coefficient of variation of signal intensity based on the error model built in the Applied Biosystems image analysis software
FLAG quality of each probe
DETECTION FLAG Detectable: 1 (S2N>3 and FLAG < 5000); not detectable: 0 (S2N<3 or FLAG>5000)
UNF_VALUE Signal normalized using the quantile-quantile method (www.bioconductor.org)

Data table
ID_REF VALUE SIGNAL_RAW STDEV S2N CV FLAG DETECTION FLAG UNF_VALUE
297784 71693 41581.1 483.6 86 0.055 1 1 71693
297907 141.9 141.9 -0.4 2.362 1 0 184
297912 17392 9736.7 486.8 20 0.074 1 1 17392
297935 315.4 315.4 0.8 1.244 1 0 438
297990 1586.5 543.8 2.9 0.347 1 0 2823
297993 137.1 137.1 -2.7 0.381 1 0 177
298000 133870 79479 702.2 113.2 0.04 1 1 133870
298038 240.6 240.6 0.4 2.414 1 0 316
298121 338.2 338.2 -1.7 0.573 1 0 477
298130 853.7 533.6 1.6 0.626 1 0 1467
298143 7843 4363.7 387.5 11.3 0.104 1 1 7843
298150 238.5 238.5 -0.9 1.125 1 0 312
298151 274.9 274.9 0.6 1.627 1 0 371
298155 463.9 215.7 2.2 0.467 1 0 717
298165 8000 4433.6 170.6 26 0.055 1 1 8000
298174 5289 2921.3 251.1 11.6 0.094 1 1 5289
298188 205.8 205.8 -1.7 0.592 1 0 266
298200 182439 109176.6 1706 64 0.056 1 1 182439
298246 17515 9809 467.1 21 0.062 1 1 17515
298248 232 232 -0.3 3.366 1 0 302

Total number of rows: 33012

Table truncated, full table size 1363 Kbytes.




Supplementary data files not provided

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