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Sample GSM265359 Query DataSets for GSM265359
Status Public on Dec 10, 2008
Title StrainSM_M_HF_Rep2
Sample type RNA
 
Source name Strain SM, Males, HF Diet
Organism Mus musculus
Characteristics Strain: SM
Sex: Male
Diet: 30% fat
Biological Replicate: 2
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 8.607192632
1415671_at 10.15469194
1415672_at 10.3867551
1415673_at 7.647933087
1415674_a_at 8.338908599
1415675_at 8.177140315
1415676_a_at 10.49379603
1415677_at 10.26147739
1415678_at 10.02129322
1415679_at 10.43126326
1415680_at 8.053786339
1415681_at 9.425791005
1415682_at 7.26056173
1415683_at 10.45885973
1415684_at 8.417607716
1415685_at 8.885151009
1415686_at 9.324076131
1415687_a_at 11.53026541
1415688_at 10.45395505
1415689_s_at 8.024262076

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM265359.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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