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Sample GSM473331 Query DataSets for GSM473331
Status Public on Aug 18, 2011
Title SD-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 standard AIN-93G dirt, (SD).
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 107.486 -0.338
ILMN_1212612 120.249 -0.244
ILMN_1212619 57.908 -0.856
ILMN_1212628 67.301 -0.730
ILMN_1212632 195.437 0.162
ILMN_1212636 1312.614 1.755
ILMN_1212637 3287.301 2.523
ILMN_1212645 4773.589 2.835
ILMN_1212648 212.281 0.231
ILMN_1212653 93.084 -0.459
ILMN_1212672 284.001 0.474
ILMN_1212682 97.105 -0.423
ILMN_1212683 60.147 -0.824
ILMN_1212685 74.421 -0.646
ILMN_1212692 83.035 -0.554
ILMN_1212693 150.066 -0.059
ILMN_1212695 84.243 -0.542
ILMN_1212698 64.542 -0.765
ILMN_1212702 10579.130 3.500
ILMN_1212703 233.670 0.311

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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