|
| Status |
Public on Sep 09, 2009 |
| Title |
WT Arabidopsis seedlings replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
WT
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col0
age: 12 days old seedlings
|
| Treatment protocol |
Samples were collected at Zeitgeber Time 15 (ZT15).
|
| Growth protocol |
Seedlings were grown on MS3 medium under 12-hour light:12-hour dark (LD) cycles for 12 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extractions were performed with Pure Link Total RNA Purification System (Invitrogen).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual Rev. 3, 2005, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix 7G Scanner using AGCC software version 1.1
|
| Description |
Genome expression data from WT Arabidopsis seedlings
|
| Data processing |
Carmaweb software (https://carmaweb.genome.tugraz.at) was used for data processing with the gcRMA algorythm for normalization. Differentially expressed genes were identified using the empirical Bayes moderated t statistics from the LiMMA package. Genes with an FDR < 5% were selected as misregulated in TOC1-ox
|
| |
|
| Submission date |
Sep 08, 2009 |
| Last update date |
Sep 08, 2009 |
| Contact name |
Paloma Mas |
| E-mail(s) |
pmmgmc@cid.csic.es
|
| Phone |
34-93-400-6100
|
| Organization name |
Consorcio CSIC-IRTA-UAB (CRAG)
|
| Department |
Genetica Molecular
|
| Street address |
C/ Jordi Girona 18-26
|
| City |
Barcelona |
| ZIP/Postal code |
08034 |
| Country |
Spain |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE18007 |
Genome-wide analysis of TOC1-ox transcriptional networks |
|
