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Sample GSM1139928 Query DataSets for GSM1139928
Status Public on Apr 25, 2014
Title Liver-Ad Lib- Homozygous knockout-replicate 2
Sample type RNA
Source name Liver-Ad Lib- Homozygous knockout
Organism Mus musculus
Characteristics strain: C57BL/6J
agender: male
age: 2-5 months old
agenotype: Homozygous knockout (SIRT1-/-)
treatment: Ad libitum diet
Treatment protocol Mice were feed either a 40% caloric restricted (CR) diet or an ad libitum (AL) diet until they reached 13-16 months at which time they were sacrificed, and the livers were collected and flash frozen.
Growth protocol 2-5 month old C57BL/6J male mice were housed following 1 of 2 dietary protocols
Extracted molecule total RNA
Extraction protocol RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions and homogenized using a polytron. Quantity and quality of the RNA was assessed using the Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips.
Label biotin
Label protocol Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5ug 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 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix MouseRef-8 v2 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 biotin 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 Liver-Ad Lib- Homozygous knockout
Data processing Data was extracted using the Illumina BeadStudio software(v3.4.0). Any spots at or below the background were filtered out using an Illumina detection p value of 0.02 and above. The natural log of all remaining scores 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 file.
Submission date May 14, 2013
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)
GSE46895 SIRT1 but not its increased expression is essential for lifespan extension in caloric restricted mice.

Data table header descriptions
VALUE Z_VALUE = Z transformation of the natural log of the raw intensity values
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 -0.401031066 0.09273183
ILMN_1212612 0.414372819 0
ILMN_1212619 -0.722507243 0.6754386
ILMN_1212628 -0.730685701 0.7030075
ILMN_1212632 -0.252815831 0.03258145
ILMN_1212636 2.195252782 0
ILMN_1212637 1.359492933 0
ILMN_1212645 3.121549008 0
ILMN_1212648 0.254421978 0
ILMN_1212653 -0.396189192 0.08897243
ILMN_1212672 0.559385598 0
ILMN_1212682 -0.429720662 0.1065163
ILMN_1212683 -0.736615841 0.7192982
ILMN_1212685 -0.714012135 0.641604
ILMN_1212692 -0.645885705 0.4235589
ILMN_1212693 0.235722955 0
ILMN_1212695 -0.629643742 0.3847118
ILMN_1212698 -0.785786904 0.8709273
ILMN_1212702 4.462575611 0
ILMN_1212703 0.432406455 0

Total number of rows: 25697

Table truncated, full table size 836 Kbytes.

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

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