|
| Status |
Public on Aug 01, 2013 |
| Title |
7-Old AL |
| Sample type |
RNA |
| |
|
| Source name |
Rattus norvegicus (Fischer-344), vastus lateralis muscle
|
| Organism |
Rattus norvegicus |
| Characteristics |
diet: AL
strain: Fischer-344
tissue: vastus lateralis muscle
|
| Treatment protocol |
2 month old male Fischer-344 rats were assigned to the ad libitum (AL) group, and fed(AL) throughout their lifespan. All animals were fed a NIH-31 standard chow (Harlan Teklad, Indianapolis, IN, USA). Rats were singly housed in an environmentally controlled vivarium with unlimited access to water and a controlled photoperiod (12 hr. light;12 hr. dark). Body weights and food intake were recorded biweekly. All rats were maintained between 68-72°F according to animal protocols and NIH guidelines.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from skeletal muscle samples using Trizol Reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions. The RNA quality and quantity was checked using an Agilent 2100 Bio-analyzer and the RNA 6000 nano-chips (Agilent Technologies, Palo Alto, CA).
|
| Label |
Streptavidin-Cy3 bound to the 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 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Sentrix Rat Ref-12,v1 Expression BeadChips (Illumina, San Diego, CA). Each BeadChip has 22,000 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 |
Animals at 27 months of age were sacrificed and the vastus lateralis muscle was flash frozen.
Rattus norvegicus (Fischer-344), vastus lateralis muscle from animals maintained on AL feeding from 2-27 months of age.
|
| Data processing |
Data was extracted using the Illumina GenomeStudio Gene Expression 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 values is included in the supplemental file.
|
| |
|
| Submission date |
May 20, 2012 |
| 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 |
GPL10239 |
| Series (2) |
| GSE38062 |
Comparison of the long-term effects of calorie restriction without malnutrition on global gene expression profiles of rat and human skeletal muscle [Rat] |
| GSE38063 |
Comparison of the long-term effects of calorie restriction without malnutrition on global gene expression profiles of rat and human skeletal muscle |
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