disease state: tibial muscular dystrophy (TMD) tissue: tibialis posterior age at biopsy: 52 Sex: male
Extracted molecule
total RNA
Extraction protocol
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA using two-cycle amplification (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2.0 Arrays.
Scan protocol
Arrays were scanned using GeneChip Scanner 3000.
Description
T6-TMD
Data processing
Expression values were determined using Affymetrix Microarray Suite 5.0. GeneSpring GX version 11.0 was used to analyze the data using MAS5.0 normalization with all probes with absent flags removed from the data. The data was baseline transformed to the median of all samples. The condition average signal for each probe was filtered by significance using an unpaired t-test with unequal variance (Welch correction, P<0.05) using multiple testing correction (Benjamini-Hochberg), followed by a two-fold change cut-off.
