|
| Status |
Public on Jun 13, 2008 |
| Title |
CRUSH 3D B |
| Sample type |
RNA |
| |
|
| Source name |
retinas 3d post IONC
|
| Organism |
Rattus norvegicus |
| Characteristics |
time and injury 3d post IONC
|
| Treatment protocol |
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 retinas 3d post IONC rep 2
|
| 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).
|
| |
|
| Submission date |
Dec 17, 2007 |
| Last update date |
Jun 13, 2008 |
| Contact name |
MARTA AGUDO |
| E-mail(s) |
[email protected]
|
| Organization name |
MURCIA UNIVERSITY
|
| Department |
OFTALMOLOGY
|
| Street address |
FACULTAD MEDICINA, CAMPUS ESPINARDO
|
| City |
MURCIA |
| ZIP/Postal code |
30100 |
| Country |
Spain |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE9918 |
temporal profiling of retinal transcriptome regulation after IONT and IONC |
|
