Skin biopsies placed in RNAlater at bedside were stored at -80 degrees C until processing. RNA was extracted by homogenization in RLT Buffer and purifying over RNeasy columns.
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol
The labeled, fragmented DNA was hybridized to the GeneChip HG-U133A 2.0 Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix Fluidics Station 450.
Scan protocol
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).
Description
RL_D6_N10-11
Data processing
Processed using affy package for R, using MAS5 normalization. Log2_batch_adjusted.txt: Log2 data in this matrix was adjusted for batch differences using the ComBat algorithm within the sva package for R. Brainarray custom CDF for HGU133A2 (version 19.0.0, ENTREZG) was utilized for this data set. http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/19.0.0/entrezg.asp
