naive rats were not treated. IONT rats underwent introorbital nerve transection, IONC rats intraorbital nerve crush
Growth protocol
Rats were kept in standard housing condintions
Extracted molecule
total RNA
Extraction protocol
Trizol extraction of total RNA was performed according to the manufacturer's instructions and was following by a further cleansing step through RNAeasy mini kit columns (Quiagen)
Label
biotin
Label protocol
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2003, Affymetrix).
Hybridization protocol
Following fragmentation, 15 ug of cRNA were hybridized on Rat norvergicous Affymetrix GeneChip Rat Genome 230 2.0 Array
Scan protocol
Gene Chip Operating software, (GCOS 1.3 Afffymetrix, Santa Clara CA)
Description
RNA from naive adult rat retina rep 5
Data processing
Data were processing using Bioconductor software, normalization was done with the GCRMA package. IONT and IONC samples at each time point were compared to naive ones. Significantly regulated sequences were extracted using the limma package (Bvalue>0, pvalueFDR<0,01) and the maSigPro package for time course series (pvalueFDR<0,01, Rsquared treshold=0,6).Log2 output values of regulated sequences were transformed to their net (fold change) values. Control level of expresion was set to 1, above 1 are up-regulated sequences and below 1 to 0 downregulated (when a RNA is not present its value is not negative but 0).
