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Status |
Public on Jul 07, 2013 |
Title |
rsa1 salt 12 h rep3 |
Sample type |
RNA |
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|
Source name |
Arabidopsis rsa1-1, salt, 24 h.
|
Organism |
Arabidopsis thaliana |
Characteristics |
tissue: seedlings treatment: Salt with 120 mM NaCl for 24 h genotype: rsa1-1 genetic background: Columbia gl1 expressing RD29A::LUC transgene age: Seven-day-old
|
Treatment protocol |
Six-day-old wild type and rsa1-1 mutant plants were subjuected to salt stress with 120 mM NaCl for 0 and 24 h.
|
Growth protocol |
Arabidopsis seedlings on Murashige and Skoog (MS) medium agar plates (1x MS salts, 2% sucrose, 1.2% agar, pH 5.7) were grown under cool, white light (~120 μmol m-2 s-1) at 21℃ with a 16-h-light/8-h-dark photoperiod.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted with Trizol reagent (Invitrogen) following the manufacturer's instructions.
|
Label |
biotin
|
Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 µg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
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Hybridization protocol |
Following fragmentation, 10 µg of cRNA was hybridized for 16 h at 45°C on Affymetrix ATH1 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
Description |
Gene expression data from Arabidopsis rsa1-1 plants with salt stress for 24 h
|
Data processing |
The datasets were subjected to the Robust Multiarray Averaging (RMA) normalization method. The normalized data were further analyzed and p-values were generated by the affymGUI component of Bioconductor in statistics environment R with the default parameters.Genes were selected by the RankProd (non-paramteric method based on the estimated percentage of false discoveries (p value < 0.05)) method.
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|
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Submission date |
Jul 10, 2012 |
Last update date |
Aug 15, 2018 |
Contact name |
Jianhua Zhu |
Phone |
3014050920
|
Organization name |
University of Maryland
|
Department |
Plant Science and Landscape Architecture
|
Street address |
2102 Plant Sciences Building
|
City |
College Park |
State/province |
MD |
ZIP/Postal code |
20742 |
Country |
USA |
|
|
Platform ID |
GPL198 |
Series (1) |
GSE39236 |
The rsa1-1 mutation affects global gene expression in Arabidopsis thaliana with or without salt stress |
|
Relations |
Reanalyzed by |
GSE118579 |