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Sample GSM473334 Query DataSets for GSM473334
Status Public on Aug 18, 2011
Title HFD-2
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 100.578 -0.369
ILMN_1212612 209.076 0.252
ILMN_1212619 67.503 -0.707
ILMN_1212628 65.545 -0.732
ILMN_1212632 140.915 -0.083
ILMN_1212636 1205.078 1.737
ILMN_1212637 2435.709 2.334
ILMN_1212645 4339.452 2.823
ILMN_1212648 150.189 -0.029
ILMN_1212653 116.877 -0.242
ILMN_1212672 228.162 0.326
ILMN_1212682 83.844 -0.523
ILMN_1212683 60.478 -0.800
ILMN_1212685 64.141 -0.750
ILMN_1212692 86.997 -0.492
ILMN_1212693 170.328 0.078
ILMN_1212695 73.594 -0.634
ILMN_1212698 66.755 -0.716
ILMN_1212702 18542.680 4.055
ILMN_1212703 256.656 0.426

Total number of rows: 25697

Table truncated, full table size 682 Kbytes.




Supplementary data files not provided
Raw data included within Sample table
Raw data are available on Series record
Processed data included within Sample table

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