|
| Status |
Public on Aug 02, 2011 |
| Title |
seedling in dark treated with DEX, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis thaliana seedlings growing in dark for 4 days and treated with DEX for 2 hours
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: seedling
age: 4 days
genotype/variation: FHY3p:FHY3-GR fhy3-4 transgenic line
|
| Treatment protocol |
treated with 10 μM dexamethasone (DEX) or MOCK (equal volume of ethanol) for 2 h
|
| Growth protocol |
FHY3p:FHY3-GR fhy3-4 transgenic seedlings grown in D or continuous FR light for 4 d
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
RNA quality was assessed with an Agilent 2100 Bioanalyzer, and hybridization to the Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays was performed according to the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Data processing |
Raw microarray data were normalized using the robust multiarray analysis (RMA) algorithm in the BIOCONDUCTOR affy package. Then the microarray data were analyzed using Significance Analysis of Microarrays (SAM) method with default parameters as well as a manual setting of false discovery threshold (FDR) < 0.027 in D and <0.022 in FR.
|
| |
|
| Submission date |
Jul 15, 2011 |
| Last update date |
Aug 15, 2018 |
| Contact name |
Bosheng Li |
| E-mail(s) |
libs@sustc.edu.cn
|
| Organization name |
SUSTC (current, may different with previous institution )
|
| Department |
MCDB
|
| Street address |
SUStech Huiyuan #1 406
|
| City |
Shenzhen |
| State/province |
Guangdong |
| ZIP/Postal code |
581055 |
| Country |
China |
| |
|
| Platform ID |
GPL198 |
| Series (2) |
| GSE30712 |
Expression data from Arabidopsis thaliana under dark and far-red light |
| GSE30713 |
Genome-wide Binding Site Analysis of FAR-RED ELONGATED HYPOCOTYL 3 Reveals Its Novel Function in Arabidopsis Development |
|
| Relations |
| Reanalyzed by |
GSE118579 |
