8 protocols
AccessionType
bioassay_data_transformation
ID_REF =
VALUE = generalized logarithm transformed values
feature_extraction
Data were converted from .cel files and averaged across probes within each probeset using the Bioconductor package affy (version 1.22.1) within the statistical software system R (version 2.10.1), then transformed via a generalized logarithm transformation using the Bioconductor package LMGene (version 2.4.0).
image_aquisition
Affymetrix GeneChip Scanner 3000 7G
feature_extraction
Software: Affymetrix Genechip Command Console (AGCC)
feature_extraction
A one-way analysis of variance (ANOVA) model was fitted to the data one probeset at a time. For probeset for which the global F test was significant at the 5% level, indicating significant differences between at least two levels of the factor, Tukey HSD post-hoc tests were conducted to test for significant differences among the comparisons of interest.
nucleic_acid_extraction
TRIzol (Invitrogen) extraction of total RNA
labeling
3’ IVT express kit (Affymetrix ) was used to biotin label 250 ng of total RNA.
hybridization
Affymetrix GeneChip Hybridization Oven 640, Affymetrix GeneChip Fluidics Station 450