|
| Status |
Public on Mar 07, 2007 |
| Title |
wild-type Arabidopsis, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
leaves from wild-type Arabidopsis plants, soil-grown for 30 days
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Genotype: wild-type Columbia background
30 day-old soil grown plants
|
| Growth protocol |
Arabidopsis plants were seeded and grown in soil at 22-26 °C in an 8 hr light/16 hr dark regime (under Phillips F40CW 34W fluorescent lights, with an intensity of 55 µmol m-2 sec-1).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the Invitrogen Trizol Reagent (cat 15596-018) and further purified with the Qiagen RNeasy Plant Mini Kit (cat 74903), and tested for quality by gel electrophoresis and inspection of the stable RNA bands.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 4 ug total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, 20 ug of biotin-labeled cRNA were hybridized for 16 hr at 45C on the ATH1-121501 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GCS 3000 7G scanner.
|
| Description |
Gene expression data from wild-type plants
|
| Data processing |
The data were analyzed with ArrayAssist 3.2 (Stratagene) using the PLIER normalization algorithm. For this, the default settings were applied: HZ=4 VZ=4 BG=2 SmoothFactorBG=100.000000 Epsilon=0.500000 BF= Gamma1L=0.004500 Gamma1H=0.004500 Gamma2L=0.006000 Gamma2H=0.006000 Perturbation=1.100000
|
| |
|
| Submission date |
Mar 06, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Arthur G Hunt |
| E-mail(s) |
aghunt00@uky.edu
|
| Phone |
859-257-5020 ext 80776
|
| Fax |
859-257-7125
|
| Organization name |
University of Kentucky
|
| Department |
Dept. of Plant and Soil Sciences
|
| Street address |
301A Plant Science Building
|
| City |
Lexington |
| State/province |
KY |
| ZIP/Postal code |
40546-0312 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE7211 |
A polyadenylation factor subunit implicated in regulating oxidative stress responses in Arabidopsis thaliana |
|
| Relations |
| Reanalyzed by |
GSE119083 |
