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Status |
Public on Jan 16, 2013 |
Title |
Col-0 vs lsm1a lsm1b-1 |
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
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|
|
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 1 of 3. 3-week-old Arabidopsis plants exposed 1 day at 4ºC. Rep 1.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.
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Submission date |
Jul 25, 2012 |
Last update date |
Jan 16, 2013 |
Contact name |
Carlos Perea-Resa |
E-mail(s) |
cperea@cib.csic.es
|
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. |
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