|
| Status |
Public on Dec 24, 2011 |
| Title |
leaf_Col_clean-air_3h_biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis leaf, Col-0 genotype, clean-air control, treated for 3 h
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Col-0
treatment: clean-air
sampling time: 3 hours
|
| Treatment protocol |
For ozone treatments, plants were transferred to four chambers located in a walk-in growth chamber in the North Carolina State University Phytotron. Temperature, relative humidity (RH) and PPFD in the chambers were 24 °C, 53% and 362 μmol m-2 s-1, respectively. Plants were treated with either 5 or 125 ppb ozone for 7 h per day for two days. Leaf tissue samples from mid-whorl leaves were taken after ozone exposure for 3 h and 2 d, and then frozen in liquid nitrogen for later analysis.
|
| Growth protocol |
Columbia wild-type and G-protein null mutant gpa1-4/agb1-2 plants sown in Metro-Mix were germinated under a photosynthetic photon flux density (PPFD) of 400 µmol m-2 s-1 (9 h light/15 h dark cycle) at 23 °C in a growth chamber in the North Carolina State University Phytotron. Plants were grown for 4-5 weeks in the growth chamber. Plants were fertilized with Phytotron nutrient solution (Downs & Thomas, 1983) once per week.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was performed using Qiagen RNeasy mini kits according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
The MessageAmp II-Biotin Enhanced Kit (Ambion, Invitrogen Corp, Carlsbad, CA) was used to generate biotinylated aRNA from the cDNA reaction.
|
| |
|
| Hybridization protocol |
Fragmented aRNA (15 µg) was added to a hybridization cocktail (0.05 µg µl-1 fragmented cRNA, 50 pM control oligonucleotide B2, BioB, BioC, BioD and cre hybridization controls, 0.1 mg ml-1 herring sperm DNA, 0.5 mg ml-1 acetylated BSA, 100 mM MES, 1 M [Na+], 20 mM EDTA and 0.01% Tween 20). aRNA (10 µg) was used for hybridization in a volume of 200 µl per slide. Affymetrix arrays were hybridized for 16 h at 45 °C in a GeneChip Hybridization Oven 640 (Affymetrix).
|
| Scan protocol |
GeneChips were scanned using GeneChip Scanner 3000 7G Plus.
|
| Data processing |
Affymetrix GeneChip Operating Software was used for washing, scanning and basic analysis. Affymetrix Expression Console software processed the CEL files. The software uses the RMA algorithm.
|
| |
|
| Submission date |
Dec 22, 2011 |
| Last update date |
Aug 15, 2018 |
| Contact name |
Fitzgerald Lewis Booker |
| E-mail(s) |
[email protected]
|
| Phone |
919-515-9495
|
| Fax |
919-856-4598
|
| URL |
http://www.ars.usda.gov/saa/psru
|
| Organization name |
USDA-ARS
|
| Department |
Plant Science Research
|
| Lab |
Air Quality/Climate Change
|
| Street address |
3127 Ligon Street
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27607 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE34667 |
Expression data from ozone-treated wild-type and G-protein null mutant Arabidopsis lines |
|
| Relations |
| Reanalyzed by |
GSE118579 |
