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Sample GSM473335 Query DataSets for GSM473335
Status Public on Aug 18, 2011
Title HFD-3
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 108.690 -0.293
ILMN_1212612 198.560 0.220
ILMN_1212619 64.608 -0.735
ILMN_1212628 62.887 -0.758
ILMN_1212632 134.803 -0.109
ILMN_1212636 1097.397 1.675
ILMN_1212637 2357.581 2.326
ILMN_1212645 3525.803 2.668
ILMN_1212648 140.968 -0.071
ILMN_1212653 103.571 -0.334
ILMN_1212672 222.770 0.318
ILMN_1212682 70.188 -0.665
ILMN_1212683 59.517 -0.805
ILMN_1212685 69.626 -0.672
ILMN_1212692 80.837 -0.545
ILMN_1212693 161.991 0.047
ILMN_1212695 79.509 -0.559
ILMN_1212698 55.887 -0.859
ILMN_1212702 25348.710 4.347
ILMN_1212703 276.987 0.503

Total number of rows: 25697

Table truncated, full table size 682 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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