|
| Status |
Public on Sep 20, 2017 |
| Title |
Vastus lateralis muscle_Old_replicate_1_rat |
| Sample type |
RNA |
| |
|
| Source name |
Vastus lateralis muscle_Old
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Fisher-344
tissue: Muscle
Sex: Male
age: Old
|
| Growth protocol |
Experimental protocol: Young (N=5, 5 months), middle-aged (N=5, 17 months), and old (N=5, 30 months) male skeletal muscle samples from Fisher-344 rats were used in this study. Rats were fed a standard NIH-31 chow (Harlan Teklad, Indianapolis, IN, USA) and were singly housed in an environmentally controlled vivarium with unlimited access to water. Animal rooms were maintained at 20-22 oC with 30-70% relative humidity and a 12-hour light/dark cycle according to animal protocols and NIH guidelines. Vastus lateralis muscles were harvested from rats. Muscle samples were flash frozen in liquid nitrogen and stored at -80oC until assayed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from skeletal muscle using Trizol Reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions
|
| Label |
Cy3
|
| Label protocol |
Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg 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 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina's HumanHT-12 V4.0 Expression Bead Chips (Illumina, San Diego, CA). Each BeadChip has more than 47,000 probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI) RefSeq Release 38 (November 7, 2009) and other sources. 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 0.8 μm using the Illumina BeadArray scanner.
|
| Description |
Sample name: 6-O_AL
|
| Data processing |
Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue 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 is supplied. ID_REF = Unique identifiers from GPL6101; Z_VALUE = Z transformation of the natural log of the raw intensity values; Detection_Pval = Detection Pvalue from Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0.
|
| |
|
| Submission date |
Sep 19, 2016 |
| 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 |
GPL6101 |
| Series (2) |
| GSE87107 |
Conserved and species specific molecular denominators in mammalian aging [rat] |
| GSE87109 |
Conserved and species-specific molecular denominators in mammalian skeletal muscle aging |
|
