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Sample GSM1191955 Query DataSets for GSM1191955
Status Public on Sep 22, 2014
Title Muscle_Standard Diet_Replicate #2
Sample type RNA
 
Source name Muscle_Standard Diet
Organism Mus musculus
Characteristics strain: C57BL/6J
gender: male
tissue: Muscle
treatment: standard AIN-93G diet (SD)
Treatment protocol Diets were started at 28 weeks of age after randomization into two groups of 100 mice each. Mice were fed either a standard AIN-93G diet (SD; carbohydrate:protein:fat ratio of 64:19:17 percent of kcal), or a SD supplemented with SRT2104. SRT2104 was added at a dose of 1.33 g drug per kg of chow, formulated to provide daily doses of approximately 100 mg drug per kg body weight to the mice.
Growth protocol Male C57BL/6J mice were started on two different diets at 28 weeks of age after randomization into two groups of 100 mice per group. Mice were placed into a standard diet group and a standard diet plus SRT2104 group. Mice were allowed to live to the end of their lives.
Extracted molecule total RNA
Extraction protocol At the end of their life, muscle and liver tissue was harvested and snap frozen. RNA was extracted from both tissues using 1.0mm glass beads in a Precellys 24 Tissue Homogenizer and Qiagen RNeasy Mini Kits for the liver tissue or the RNeasy Fibrous Tissue kit for the muscle tissue according to manufacturer's specifications. Quality and quantity of the total RNA was checked with the Agilent 2100 bioanalyzer using RNA 6000 Nano chips.
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, 0.5ug 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 Muscle_Standard Diet_Replicate #2
Data processing Data was extracted using the Illumina GenomeStudio software(v1.6.0). 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.
Detection_Pval = Detection Pvalue from Illumina GenomeStudio software, ver 1.6.0.
 
Submission date Jul 18, 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 (2)
GSE49000 SRT2104 extends survival of male mice on a standard diet and preserves bone and muscle mass
GSE50987 The SIRT1 activator SRT1720 extends lifespan and improves health of mice fed a standard diet

Data table header descriptions
ID_REF
VALUE Z transformation of the natural log of the raw intensity values
Detection Pval Detection Pvalue from Illumina GenomeStudio software, ver 1.6.0.

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 -0.525069011 0.2807
ILMN_1212612 1.355920338 0
ILMN_1212619 -0.571978058 0.49123
ILMN_1212628 -0.622730606 0.7218
ILMN_1212632 -0.393647607 0.03258
ILMN_1212636 2.253408699 0
ILMN_1212637 0.609218476 0
ILMN_1212645 -0.619155498 0.70426
ILMN_1212648 0.202611808 0
ILMN_1212653 -0.21350212 0.00251
ILMN_1212672 0.342407457 0
ILMN_1212682 -0.645337809 0.80075
ILMN_1212683 -0.597066392 0.599
ILMN_1212685 -0.534129286 0.31579
ILMN_1212692 -0.523429547 0.27945
ILMN_1212693 -0.634429292 0.76316
ILMN_1212695 -0.585750231 0.55639
ILMN_1212698 -0.576263668 0.51629
ILMN_1212702 4.241428802 0
ILMN_1212703 -0.078019702 0

Total number of rows: 25697

Table truncated, full table size 791 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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