NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM473332 Query DataSets for GSM473332
Status Public on Aug 18, 2011
Title SD-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 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 107.665 -0.285
ILMN_1212612 101.698 -0.333
ILMN_1212619 61.869 -0.756
ILMN_1212628 67.221 -0.686
ILMN_1212632 96.085 -0.382
ILMN_1212636 1163.272 1.741
ILMN_1212637 2678.923 2.451
ILMN_1212645 4782.885 2.944
ILMN_1212648 166.941 0.088
ILMN_1212653 94.588 -0.395
ILMN_1212672 226.441 0.348
ILMN_1212682 101.615 -0.334
ILMN_1212683 64.573 -0.720
ILMN_1212685 71.044 -0.639
ILMN_1212692 80.657 -0.531
ILMN_1212693 198.705 0.237
ILMN_1212695 78.823 -0.550
ILMN_1212698 61.626 -0.760
ILMN_1212702 12978.480 3.794
ILMN_1212703 249.654 0.431

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap