|
| Status |
Public on Sep 20, 2007 |
| Title |
S9_Muscle_Insulin_240min |
| Sample type |
RNA |
| |
|
| Source name |
Vastus Lateralis Muscle at 240 min
|
| Organism |
Homo sapiens |
| Characteristics |
Gender: Male
Diabetes Status: Family History Negative
Ethnicity: Mexican American
|
| Treatment protocol |
All subjects received a vastus lateralis muscle biopsy followed by a 180-min euglycemic, hyperinsulinemic (80 mU/m2.min) clamp, which was performed with infusion of 3-3H-glucose (prime=25 Ci, continuous infusion=0.25 Ci/min) to determine rates of glucose appearance and disposal, as previously described (DeFronzo, 1979). Biopsies of the vastus lateralis muscle were taken basally and at 30 and 240 minutes after the start of the insulin infusion, as previously described (Cusi 2000)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Muscle biopsies from each subject were homogenized in RNAStat solution (Tel-Test Inc., Friendswood, TX), using a Polytron homogenizer (Brinkmann Instruments Westbury, NY). Total RNA was purified with RNeasy and DNase I treatment (Qiagen, Chatsworth, CA).
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). A description of the protocol has been described previously (Richardson 2005)
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 using protocol EukGE-ES2.
|
| Scan protocol |
The intensity of bound dye was measured with an argon laser confocal scanner (GeneArray scanner G2500A; Agilent).
|
| Description |
Gene expression data from skeletal muscle following 240 minutes of a insulin infusion (80 mU clamp)
|
| Data processing |
The Affymetrix data acquisition programs in GCOS automatically generate a cell intensity file (CEL) from the stored images that contain a single intensity value for each probe cell on the array. The CEL files were imported into the R software package (http://www.r-project.org) and the probe level data were converted to expression measures using the Affy package from Bioconductor. Expression values for each mRNA were obtained by GC-Robust Multi-Array Analysis (GCRMA). CEL files were normalized together and the expression values obtained were submitted to analysis with linear models of microarray data (LIMMA) to identify genes that were significantly increased or decreased with a false discovery rate (FDR) of less than 5%, and a fold change of greater than 1.5.
|
| |
|
| Submission date |
Sep 19, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Dawn K Coletta |
| E-mail(s) |
[email protected]
|
| Phone |
210-567-0336
|
| Fax |
210-567-6554
|
| Organization name |
UTHSCSA
|
| Department |
Medicine
|
| Lab |
Diabetes
|
| Street address |
7703 Floyd Curl Drive
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE9105 |
Effect of Acute Physiologic Hyperinsulinemia on Gene Expression in Human Skeletal Muscle in vivo |
|
