|
| Status |
Public on Jan 16, 2013 |
| Title |
Col-0 vs lsm1a lsm1b-3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
lsm1a lsm1b
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: lsm1a lsm1b
age: 2-week-old
tissue: Rosette
|
| Growth protocol |
Plants were grown in pots containing a mixture of organic substrate and vermiculite (3:1 v/v) for two weeks in 16h light/8 h dark at 22ºC conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions. Then, total RNA was purified using the Rneasy MiniKit from QIAGEN following manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5 and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop
|
| |
|
| Channel 2 |
| Source name |
Col-0
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: control
age: 2-week-old
tissue: Rosette
|
| Growth protocol |
Plants were grown in pots containing a mixture of organic substrate and vermiculite (3:1 v/v) for two weeks in 16h light/8 h dark at 22ºC conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions. Then, total RNA was purified using the Rneasy MiniKit from QIAGEN following manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
5 ug of aminoallyl-labeled aRNA were resuspended in 0.1 M Na2CO3 (pH 9.0) and labeled with Hyper5 and Cy3 Mono NHS Ester (CyTMDye Post-labeling Reactive Dye Pack, Amersham). Samples were purified following the manufacturer's instructions for Megaclear TM (Ambion) and Hyper5 and Cy3 incorporation was measured using 1 ul of the probe in the Nanodrop
|
| |
|
| |
| Hybridization protocol |
The hybridization experiment was performed according to the manufacture's protocol (Agilent technologies, Agilent 60-mer oligo microarray processing protocol: Two color microarray based gene expression analysis, G4140-90050 ver 5.7)
|
| Scan protocol |
Images from Cy3 and Hyper5 channels were equilibrated and captured with a GenePix 4000B (Axon) and spots were converted into numerical data using GenPix software (Axon).
|
| Description |
Biological replicate 3 of 3. 3-week-old Arabidopsis plants exposed 1 day at 4ºC.
Rep 3.gpr
|
| Data processing |
Raw intensities were background-substracted by NORMEXP method with a offset of 50. Signals (in log2 scale) were then normalized by LOWESS algorithm (intra-arrays normalization) followed by adjustment of their quantiles (inter-arrays normalization). Limma software was used for the normalization.
|
| |
|
| Submission date |
Jul 25, 2012 |
| Last update date |
Jan 16, 2013 |
| Contact name |
Carlos Perea-Resa |
| E-mail(s) |
[email protected]
|
| Organization name |
CIB-CSIC
|
| Street address |
Ramiro de Maeztu,9
|
| City |
Madrid |
| ZIP/Postal code |
28040 |
| Country |
Spain |
| |
|
| Platform ID |
GPL12621 |
| Series (1) |
| GSE39630 |
Transcriptional Analysis of lsm1a lsm1b Arabidopsis mutant. |
|
