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Sample GSM526762 Query DataSets for GSM526762
Status Public on Jun 21, 2010
Title DIO_CB1R-/-_KO_vehicle_eWAT_42
Sample type RNA
 
Source name eWAT
Organism Mus musculus
Characteristics strain: C57BL/6
diet: high fat
genotype/variation: CB1R-/- (KO)
treatment: vehicle
tissue: epididymal white adipose tissue (eWAT)
Extracted molecule total RNA
Extraction protocol Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.
Label Biotin is incorporated during the amplification. This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.
Label protocol The final in vitro transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cRNA.
 
Hybridization protocol GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45°C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.
Scan protocol Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.
Description DIO CB1R-/- KO vehicle (n=3) Virtual Pool vs. DIO_CB1R-/-_KO_vehicle_eWAT_42
Data processing Data were processed using the Rosetta Resolver® system. The software performs error modeling using the data loaded and processed into the Resolver system. The Resolver system applies the RMA algorithm to combine replicates of the same sequence in an array. Affymetrix's MAS-5 method is applied to calculate a P-value for such sequences. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds of a P-value below which, genes are considered to be significantly expressed. Errors for the RMA-computed sequences are fitted using methodology developed by Rosetta using the guidelines set in Weng et al. (2006) Bioinformatics 22:1111-1121. The Resolver system also combines multiple arrays using an averaging process. The P-values for the combined results are also the combination of individual probe-level P-values (geometric means). Ratios and their P-values are computed as described in section 2.2 of Weng et al. (2006).
 
Submission date Mar 25, 2010
Last update date Jun 21, 2010
Contact name Olivia Fong
E-mail(s) olivia.fong@merck.com
Organization name Merck & Co.
Department Molecular Profiling
Lab Merck Research Laboratories
Street address P.O. Box 2000
City Rahway
State/province NJ
ZIP/Postal code 07065
Country USA
 
Platform ID GPL9734
Series (1)
GSE21069 Genome-wide expression profiling revealed peripheral effects of CB1 inverse agonists in improving insulin sensitivity and metabolic parameters

Data table header descriptions
ID_REF
VALUE Normalized signal intensities
LogRatio Log Ratios between replicate and virtual pool of control samples
Pvalue P-value of Log Ratio

Data table
ID_REF VALUE LogRatio Pvalue
100113564_TGI_at 9.983045 -0.000537 9.964451e-001
100087246_TGI_at 525.904907 -0.030691 4.202543e-001
100118487_TGI_at 25.352947 0.038286 6.227700e-001
100098414_TGI_at 33.102650 0.058970 4.178761e-001
100093140_TGI_at 49.991798 0.030051 5.991246e-001
100096868_TGI_at 311.684418 -0.020659 6.417465e-001
100110141_TGI_at 7.492886 0.036921 8.140790e-001
100115501_TGI_at 26.190121 -0.027482 6.923422e-001
100094903_TGI_at 8.660308 -0.039258 7.630003e-001
100113524_TGI_at 1373.342041 -0.022745 5.865402e-001
100093330_TGI_at 36.801826 0.076384 2.957792e-001
100113914_TGI_at 54.334938 0.041874 4.935578e-001
100100289_TGI_at 64.721428 0.042181 4.405302e-001
100114354_TGI_at 41.916275 0.021283 7.170389e-001
100112279_TGI_at 214.425583 -0.036911 4.241766e-001
100085470_TGI_at 7.579604 -0.015110 9.171127e-001
100109262_TGI_at 8.663177 0.011952 9.297556e-001
100085458_TGI_at 79.920158 0.001186 9.807774e-001
100086663_TGI_at 106.576454 0.031925 5.885299e-001
100097327_TGI_at 28186.724609 0.006143 8.600025e-001

Total number of rows: 38385

Table truncated, full table size 1904 Kbytes.




Supplementary file Size Download File type/resource
GSM526762.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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