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Sample GSM201772 Query DataSets for GSM201772
Status Public on Aug 31, 2007
Title Mouse old heart w/ a-tocopherol aT-Ht-1
Sample type RNA
 
Source name Old heart
Organism Mus musculus
Characteristics strain: B6/C3H F1 hybrid
gender: male
age: 30-month-old
Biomaterial provider University of Wisconsin-Madison, Genetics
Treatment protocol This group received a diet supplemented with 1000mg/kg of α-tocopherol since the age of 15 months.
Growth protocol Male B6C3F1 mice were purchased from Harlan Sprague-Dawley at 6-7 weeks of age. Mice were housed singly in a pathogen-free facility and provided acidified water ad libitum.
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from frozen tissue using the TRIZOL reagent (Life Technologies, Grand Island, NY) and mRNA was purified from the total RNA with oligo-dT-linked oligotex resin (Qiagen, Valencia, CA). Then, double-stranded cDNA was synthesized from 1ug of mRNA using the SuperScript Choice System (Life Technologies, Grand Island, NY) with an oligo-dT primer containing a T7 RNA polymerase promoter (Genset, La Jolla, CA), purified with phenol-chloroform-isoamyl alcohol, and precipitated with pellet paint co-precipitant (Novagen, Madison, WI). Purified double-stranded cDNA was used to synthesize biotin-labeled cRNA using the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Farmingdale, NY). The biotin-labeled antisense cRNA was then purified with the RNeasy affinity column (Qiagen, Valencia, CA). After purification, biotin-labeled cRNA was fragmented randomly to sizes ranging from 35 to 200 bases.
Label aT-Ht-1
Label protocol aT: 30-month-old a-tocopherol supplemented mouse
Ht: heart
1: sample number
 
Hybridization protocol Total 10ug cRNA was placed in the gene chip. The gene chip I used for this study is the Affymetrix Murine Genome U74Av2 chips (Affymetrix, Santa Clara, CA), which covers 12,422 transcripts. Hybridization was carried out at 45ºC for 16 h with mixing on a rotisserie at 60 rpm. Following hybridization, the hybridization solutions were removed and the gene chips were be installed in a fluidics system for washes and staining.
Scan protocol After staining, the gene chips were read at a resolution of 3 μm using a Hewlett Packard GeneArray Scanner (Affymetrix, Santa Clara, CA). The averaged images collected from two scanned images were used for the analysis.
Description We used five animals per group, and hybridized each sample to independent DNA chips, because previous work from our laboratory suggests that variability between individuals is higher than variability observed in replicate hybridizations of the same samples.
Data processing GeneChip Analysis Suite 5.0 was used to analyze the image data. The Affymetrix Mouse Genome U74Av2 chip is derived from selected genes and ESTs. Each gene is represented by the use of 16 perfectly matched and mismatched (MM) control probes. The MM probes acts as specificity controls that allows the direct subtraction of both background and cross-hybridization signals. To determine the quantitative RNA abundance, the average of the differences representing PM minus MM for each gene-specific probe family is calculated, after discarding the maximum, the minimum and any outliers beyond 3 standard deviations. To minimize variability in hybridization, the global scaling method normalizes signals of each chip. The global scaling method is computational technique in which the average signal of all probe sets in one chip is scaled to a target average intensity by multiplying a scaling factor. This scaling factor is multiplied to each probe set signal to give the raw expression.
 
Submission date Jun 15, 2007
Last update date Aug 14, 2011
Contact name Sang-Kyu Park
E-mail(s) sangkyu@colorado.edu
Phone 303-492-5159
Fax 303-492-8063
Organization name University of Colorado at Boulder
Department IBG
Street address 1480 30th St.
City Boulder
State/province CO
ZIP/Postal code 80303
Country USA
 
Platform ID GPL81
Series (2)
GSE8146 Age-related transcriptional changes and the effect of dietary supplementation of vitamin E in the mouse heart
GSE8162 Age-related transcriptional changes and the effect of dietary supplementation of vitamin E in the mouse heart and brain

Data table header descriptions
ID_REF
VALUE signal intensity
ABS_CALL absent/present call

Data table
ID_REF VALUE ABS_CALL
AFFX-MurIL2_at 94.1 A
AFFX-MurIL10_at 328 A
AFFX-MurIL4_at 61.2 A
AFFX-MurFAS_at 788.2 A
AFFX-BioB-5_at 2799 P
AFFX-BioB-M_at 6018.8 P
AFFX-BioB-3_at 3128.4 P
AFFX-BioC-5_at 10426.1 P
AFFX-BioC-3_at 7279.9 P
AFFX-BioDn-5_at 8396.1 P
AFFX-BioDn-3_at 51898 P
AFFX-CreX-5_at 92511.9 P
AFFX-CreX-3_at 123161.8 P
AFFX-BioB-5_st 516.1 A
AFFX-BioB-M_st 306 A
AFFX-BioB-3_st 217.4 A
AFFX-BioC-5_st 192.3 A
AFFX-BioC-3_st 47.7 A
AFFX-BioDn-5_st 1334.5 A
AFFX-BioDn-3_st 573.6 A

Total number of rows: 12488

Table truncated, full table size 220 Kbytes.




Supplementary file Size Download File type/resource
GSM201772.CEL.gz 2.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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