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Sample GSM471748 Query DataSets for GSM471748
Status Public on Dec 16, 2009
Title muscle_subject 3_post suppliment_rep1
Sample type RNA
 
Source name vastus lateralis muscle, post supplement
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 Left Leg (Control)
4051956071_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.
 
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

Data table header descriptions
ID_REF
VALUE Signal calculated by GenomeStudio(Illumina). Normalization was carried out as per the paper.
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_10000 7.835540333 0.001412429
ILMN_10001 12.47392003 0
ILMN_10002 7.052661712 0.02118644
ILMN_10004 8.764325072 0
ILMN_10005 6.548376598 0.4251412
ILMN_10006 7.018822592 0.02824859
ILMN_10009 6.937224613 0.04378531
ILMN_1001 6.403378156 0.6878531
ILMN_10010 6.534049617 0.4449153
ILMN_10011 8.462144159 0.001412429
ILMN_10012 6.464281109 0.5748588
ILMN_10013 6.613810041 0.2740113
ILMN_10014 6.752959791 0.1410195
ILMN_10016 6.891982607 0.05932203
ILMN_1002 6.467154034 0.569209
ILMN_10020 7.700810844 0.002824859
ILMN_10021 7.609208087 0.004237288
ILMN_10022 6.770530958 0.1172316
ILMN_10023 6.689385394 0.1751412
ILMN_10024 6.684595657 0.1822034

Total number of rows: 20589

Table truncated, full table size 629 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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