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Sample GSM473333 Query DataSets for GSM473333
Status Public on Aug 18, 2011
Title HFD-1
Sample type RNA
 
Source name Mus musculus liver tissue
Organism Mus musculus
Characteristics strain: C57BL/6J, Gender: Male, Tissue: Liver, Age: 82weeks
Treatment protocol Starting at 56 weeks of age, fed a high-fat diet (HFD).
Extracted molecule total RNA
Extraction protocol RNA was extracted using Qiagen RNAeasy Mini kit
Label Streptavidin-Cy3 bound to biotin-labeled cRNA.
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 0.75?g 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 n/a
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 p-value score of 0.02 and above. 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 will be included in the supplemental files.
 
Submission date Nov 19, 2009
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 GPL6885
Series (1)
GSE19102 SRT1720 extends healthspan and lifespan in diet-induced obese mice

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_1212607 109.593 -0.331
ILMN_1212612 148.632 -0.081
ILMN_1212619 61.348 -0.808
ILMN_1212628 75.786 -0.634
ILMN_1212632 155.028 -0.046
ILMN_1212636 1376.046 1.748
ILMN_1212637 2620.181 2.278
ILMN_1212645 4249.219 2.675
ILMN_1212648 152.479 -0.060
ILMN_1212653 116.696 -0.279
ILMN_1212672 224.909 0.260
ILMN_1212682 78.950 -0.601
ILMN_1212683 61.496 -0.806
ILMN_1212685 63.851 -0.775
ILMN_1212692 79.407 -0.596
ILMN_1212693 186.734 0.107
ILMN_1212695 79.246 -0.598
ILMN_1212698 60.492 -0.820
ILMN_1212702 18870.670 3.901
ILMN_1212703 311.633 0.528

Total number of rows: 25697

Table truncated, full table size 683 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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