|
| Status |
Public on Nov 21, 2012 |
| Title |
Typically Developing Control, Gracilis, Patient Replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
Gracilis Mucle, Control
|
| Organism |
Homo sapiens |
| Characteristics |
subject: 6
disease: TD
muscle: GR
gender: F
age: 15.5
gmfcs: N/A
popliteal angle: N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rneasy Kit (Qaigen) extration of total RNA was performed
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2-5 ug total RNA
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16-18 hr at 45oC on GeneChip Human Genome U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G
|
| Data processing |
GeneSpring Software (Affymetrix, version 11.5) was used for primary analysis. Genes were denoted as present if they had a MAS5 present call on 10/40 chips. The concordance of 3 summarization algorithms were used: MAS5, RMA, and GC-RMA. Significantly altered genes were determined by a 2x2 ANOVA within GeneSpring on patient group (cerebral palsy or control patients) and muscle (gracilis or semitendinosus) with a False Discovery Rate set at 1%. This analysis was performed on each of the three summarization algorithms and the overlap of all 3 was used as the significantly different gene set. The RMA and GCRMA in log2 format values are linked to the Series record.
|
| |
|
| Submission date |
Aug 05, 2011 |
| Last update date |
Nov 21, 2012 |
| Contact name |
Lucas Robert Smith |
| E-mail(s) |
lrs001@ucsd.edu
|
| Organization name |
University of California San Diego
|
| Department |
Bioengineering
|
| Lab |
Muscle Physiology Laboratory
|
| Street address |
3350 La Jolla Village Drive Mail Code 151
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92161 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE31243 |
Transcriptional Alterations of Hamstring Muscle Contractures in Children with Cerebral Palsy |
|
