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Sample GSM309883 Query DataSets for GSM309883
Status Public on Aug 05, 2008
Title F 6A EODHR
Sample type RNA
 
Source name Fat tissue, 6A standard diet plus 0.04% resveratrol, ad libitum on alternate days (intermittant fasting)
Organism Mus musculus
Characteristics Strain: C57BL/6NIA, Gender: Male, Tissue: Fat, Age: 11months
Treatment protocol Starting at one year of age, fed a standard AIN-93G diet plus 0.04% resveratrol, ad libitum on alternate days (intermittant fasting).
Extracted molecule total RNA
Extraction protocol RNA was extracted using Qiagen RNAeasy Lipid kit
Label biotin
Label protocol standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5g of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.
 
Hybridization protocol standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 24,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the labeled cRNA was detected by staining with streptavidin-Cy3.
Scan protocol Arrays were scanned at a resolution of 0.8um using the Beadstation 500 X from Illumina.
Description Fat 6A EODHR
Data processing Data was extracted using the Illumina BeadStudio software(v1). Any spots at or below the background were filtered out using an Illumina detection score of 0.98 and below. The natural log of all remaining genes were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores provided as supplementary file.
 
Submission date Aug 04, 2008
Last update date Jun 22, 2020
Contact name Supriyo De
Organization name NIA-IRP, NIH
Department Laboratory of Genetics and Genomics
Lab Computational Biology & Genomics Core
Street address 251 Bayview Blvd
City Baltimore
State/province Maryland
ZIP/Postal code 21224
Country USA
 
Platform ID GPL6103
Series (1)
GSE11845 Resveratrol Diet Aging (Heart, Liver, Muscle and Fat Tissue)

Data table header descriptions
ID_REF
RAW_VALUE raw intensity value from Beadstudio software
VALUE Z transformation of the natural log of the raw intensity values

Data table
ID_REF RAW_VALUE VALUE
ILMN_1212602 190.9 -0.3868109
ILMN_1212605 313.4 0.21140638
ILMN_1212607 168.6 -0.5367128
ILMN_1212612 139.8 -0.7627545
ILMN_1212616
ILMN_1212619 404.9 0.52052429
ILMN_1212626 553.9 0.89864865
ILMN_1212628
ILMN_1212632 142.3 -0.7413654
ILMN_1212636 701.1 1.18303636
ILMN_1212637 1205.5 1.83708768
ILMN_1212644
ILMN_1212645 489.9 0.75048181
ILMN_1212646 450.6 0.64957281
ILMN_1212648 208.5 -0.2803894
ILMN_1212672
ILMN_1212681
ILMN_1212682
ILMN_1212683 130.9 -0.8421327
ILMN_1212685

Total number of rows: 24594

Table truncated, full table size 574 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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