|
| Status |
Public on Apr 25, 2014 |
| Title |
Liver-Ad Lib-Wt-replcate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Liver-Ad Lib-Wt
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
agender: male
age: 2-5 months old
agenotype: Wild Type (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-Wt
|
| 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. |
|
