|
| Status |
Public on Dec 16, 2009 |
| Title |
muscle_subject 3_post exercise_48hours_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
vastus lateralis muscle, post exercise, 48hours
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
age: 18
supplement: Estradiol
tissue: skeletal muscle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by homogenizing ~30 mg of skeletal muscle in 2 mL of Trizol Reagent, followed by phase separation using 200 μL of chloroform and precipitation using 500 μL of isopropyl alcohol. The RNA pellet was then washed three times in 75% ethanol and re-suspended in 15 μL DEPC-treated water. Concentration and purity was determined using a UV spectrophotometer at the absorbance of 260/280 nm (measurements were done in duplicate). RNA integrity was assessed in a randomly chosen subset of samples using agarose gel electrophoresis. RNA samples were then treated with DNA-free recombinant DNase I (Ambion Inc, Austin, TX) according to the manufacturer’s instructions. Total RNA concentration and purity were assessed by using a Nanodrop Spectrophotometer and the Agilent Bioanalyzer Nano Chip System.
|
| Label |
biotin
|
| Label protocol |
Samples which passed quality were amplified one round and biotin-labeled, using the Illumina TotalPrep Kit (Ambion) according to the manufacturer's instructions. Concentration and quality were assessed using the Nanodrop Spectrophotometer and the Agilent Bioanalyzer Nano Chip System.
|
| |
|
| Hybridization protocol |
Labeled cRNA samples were hybridized to Human Ref-8 BeadChips (Illumina) according to the manufacturer's instructions, using equipment specified by the manufacturer (Illumina).
|
| Scan protocol |
Processed arrays were read using a BeadStation array reader (Illumina) according to the manufacturer's instructions.
|
| Description |
Muscle Biopsy from Right Leg (Exercised)
4051956108_D
|
| Data processing |
Gene array data analyses were done comparing baseline, post supplementation, 3 and 48 hours post exercise using simple paired t-test on log2 expression ratios. Genes were ranked by p-value and the inference reported following adjustment for multiple testing using the FDR and the Benjamini and Hochberg method. Among those genes with an adjusted q-value (based on FDR) of <0.05, we used hierarchical clustering (based on the HOPACH algorithm to find groups of genes with similar profiles across the subjects.
|
| |
|
| Submission date |
Nov 17, 2009 |
| Last update date |
Dec 15, 2009 |
| Contact name |
Serban Ciotlos |
| E-mail(s) |
smelov@buckinstitute.org
|
| Phone |
4085068553
|
| Organization name |
Buck Institute for Research on Aging
|
| Lab |
Melov Lab
|
| Street address |
8001 Redwood Blvd
|
| City |
Novato |
| State/province |
CA |
| ZIP/Postal code |
94945 |
| Country |
USA |
| |
|
| Platform ID |
GPL6255 |
| Series (1) |
| GSE19062 |
Eccentric exercise activates novel transcriptional regulation of hypertrophic signaling pathways |
|
