|
| Status |
Public on Jul 01, 2014 |
| Title |
gul2-1 mutant, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
7d-old gul2-1 mutant seedling grown under red light
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: gul2-1 mutant
tissue: 7 day-old whole seedlings
|
| Growth protocol |
Arabidopsis seedlings of each genotype were grown in controlled environment of growth chamber. Seedlings were grown for 7 days under continuous red light.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were prepared using Quiagen Rneasy kit
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Arabidopsis (ATH1) GenChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
gul2-1-2.CEL
|
| Data processing |
All raw data from each array were processed by background correction and quantile normalization using CodeLink from the R package (Gautier et al., 2004). In addition, all array data were processed to calculate the robust multi-array average (RMA) (Irizarry et al., 2003) using AFFY (Gautier et al., 2004). Expression values were computed by applying the RMA model of probespecific correction to perfect-match probes. These corrected probe values were then subjected to quantile normalization (Bolstad et al., 2003). The resulting RMA expression values were log2 ransformed.
|
| |
|
| Submission date |
Apr 29, 2013 |
| Last update date |
Jul 01, 2014 |
| Contact name |
Sunghwa Choe |
| E-mail(s) |
shchoe@snu.ac.kr
|
| Organization name |
Seoul National University
|
| Department |
Biological sciences
|
| Lab |
Biochemical genomics
|
| Street address |
Gwanak-Gu Shillim-Dong
|
| City |
Seoul |
| ZIP/Postal code |
151-747 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE46456 |
Analysis of gene expression controlled by light and brassinosteroids |
|
