|
| Status |
Public on Jul 01, 2019 |
| Title |
A.thaliana_Col0_-ABA_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Whole seedling, 10 day-old
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
treatment: none
cultivar: Col-0
genotype: Wild-type
|
| Treatment protocol |
Treatment with ABA (100 μM) was carried out for two hours.
|
| Growth protocol |
A. thaliana plants (Col-0) were grown on 0.8% agar plates supplemented with MS salts medium and 1% sucrose under a 16h/8h ligth/dark photoperiod, at 22 ºC and 70% relative humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol reagent (Invitrogen) and purified with RNeasy Plant Kit columns (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
cDNA amplified from 10 μg of total RNA was labeled with Cy3 fluorophore.
|
| |
|
| Hybridization protocol |
Material was hybridized to Nimblegen 12x135K array slides, in duplicate, that cover the expression of 39,042 genes of A. Thaliana (4 60mer probes per gene)
|
| Scan protocol |
Slides were scanned in a DNA Micorarray Scanner G2505C (Agilent Technologies) at 532 nm and at a 3 um resolution, and TIF images imported into NimbleSan v2.6 for quantification of signal intensity
|
| Description |
NA
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleSann v 2.6. (Roche NimbleGen, Inc.)
|
| |
|
| Submission date |
Mar 12, 2013 |
| Last update date |
Jul 01, 2019 |
| Contact name |
Crisanto Gutierrez |
| E-mail(s) |
cgutierrez@cbm.csic.es
|
| Phone |
+34 911964638
|
| Organization name |
Centro de Biologia Molecular Severo Ochoa
|
| Department |
Genome Dynamics and Function
|
| Street address |
Nicolas Cabrera 1
|
| City |
Madrid |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13970 |
| Series (1) |
| GSE45038 |
Expression analysis of plants with altered GEM mRNA levels, with and without ABA treatment (2 hours). |
|
