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Sample GSM265066 Query DataSets for GSM265066
Status Public on Dec 10, 2008
Title StrainPERA_F_HF_Rep3
Sample type RNA
 
Source name Strain PERA, Females, HF Diet
Organism Mus musculus
Characteristics Strain: PERA
Sex: Female
Diet: 30% fat
Biological Replicate: 3
Extracted molecule total RNA
Extraction protocol Liver samples were extracted from each mouse as described previously (Shockley and Churchill, 2006). Total RNA was reverse transcribed with oligo(dT)-T7 primers. before double-stranded cDNA was generated with the Superscript double-stranded cDNA synthesis custom kit (Invitrogen).
Label biotin
Label protocol The cDNA was linearly amplified with biotinylated nucleotides (Enzo Diagnostics, Farmingdale, NY) through an in vitro transcription reaction with T7 RNA polymerase.
 
Hybridization protocol Fifteen micrograms of biotin-labeled and fragmented cRNA was then hybridized onto MOE430v2.0 GeneChip® arrays for 16 hours at 45°C. Post-hybridization staining and washing were performed according to the manufacturer’s protocols using the Fluidics Station 450 instrument (Affymetrix, Santa Clara, CA).
Scan protocol Arrays were scanned with a GeneChip® Scanner 3000 laser confocal slide scanner. Images were quantified using GeneChip Operating Software (GCOS) v1.2 (Affymetrix).
Description One group of mice was fed an atherogenic high-fat (30% fat) diet containing cholic acid to increase fat uptake and another was fed a low-fat (6% fat) regular chow diet. Males and females from both diets were studied for mouse strains 129S1/SvImJ, A/J, BALB/cJ, C3H/HeJ, C57BL/6J, CAST/EiJ, DBA/2J, I/LnJ, MRL/MpJ-Tnfrsf6lpr/J, NZB/BINJ, PERA/Ei, and SM/J. All strains were sacrificed between 11- and 13 weeks of age except for CAST and PERA, which were harvested after 50 weeks of age. CAST and PERA were subsequently removed from our analysis based on discrepant harvest age, but can be found in our database (see below). Three replicate animals were used for each combination of diet, strain, and sex, resulting in a total of 120 mice surveyed for gene expression.
Data processing RMA values are in the VALUE column here. Briefly, the RMA method was used to adjust the background of perfect match (PM) probes, apply a quantile normalization of the corrected PM values and calculate final expression measures using the Tukey median polish algorithm.
 
Submission date Feb 12, 2008
Last update date Aug 28, 2018
Contact name Keith Shockley
Organization name The Jackson Laboratory
Department Computational and Systems Biology
Street address 600 Main Street
City Bar Harbor
State/province ME
ZIP/Postal code 04609
Country USA
 
Platform ID GPL1261
Series (1)
GSE10493 Novartis 12 Strain Diet Sex Survey
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE RMA-calculated signal intensity

Data table
ID_REF VALUE
1415670_at 8.727482701
1415671_at 10.07815678
1415672_at 10.42317757
1415673_at 7.347777553
1415674_a_at 8.449122263
1415675_at 7.940541825
1415676_a_at 10.77478097
1415677_at 10.46797308
1415678_at 10.25729004
1415679_at 10.65059294
1415680_at 8.101110358
1415681_at 9.313505463
1415682_at 7.447534032
1415683_at 10.25542373
1415684_at 9.082796374
1415685_at 8.855001316
1415686_at 9.423083296
1415687_a_at 12.07977321
1415688_at 10.32969148
1415689_s_at 8.647291566

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM265066.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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