|
| Status |
Public on Feb 25, 2013 |
| Title |
rcf1-1_cold_24 h_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis rcf1-1, cold at 4°C, 24 h.
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
treatment: cold at 4°C
age: Fourteen-day-old
genotype/variation: rcf1-1
|
| Treatment protocol |
Fourteen-day-old wild type and rcf1-1 mutant plants were subjuected to cold stress at 4°C for 0, 12, and 24 h.
|
| Growth protocol |
Arabidopsis seedlings on Murashige and Skoog (MS) medium agar plates (1x MS salts, 2% sucrose, 0.6% agar, pH 5.7) were grown under cool, white light (~120 μmol m-2 s-1) at 21 ± 1℃ 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).
|
| |
|
| 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 rcf1-1 plants with cold 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. Normalized expression values presented in Matrix table are log2 values.
|
| |
|
| Submission date |
Jul 03, 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) |
| GSE39090 |
The rcf1-1 mutation affects global gene expression in Arabidopsis thaliana with or without cold stress. |
|
| Relations |
| Reanalyzed by |
GSE118579 |
