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Status |
Public on Dec 16, 2009 |
Title |
muscle_subject 20_baseline_rep1 |
Sample type |
RNA |
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Source name |
vastus lateralis muscle, baseline
|
Organism |
Homo sapiens |
Characteristics |
gender: Male age: 25 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.
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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.
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Description |
Muscle Biopsy from Left Leg (Control) 4051956105_A
|
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.
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|
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Submission date |
Nov 17, 2009 |
Last update date |
Dec 15, 2009 |
Contact name |
Simon Melov |
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 |
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