|
| Status |
Public on Jun 13, 2017 |
| Title |
wild type, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
WT seedlings_12 days old_10oC cold for 7days
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
accession background: No-0
genotype/variation: wild type
tissue: 12 day-old seedlings
treated at: 10oC cold for 7 days
|
| Treatment protocol |
For chilling treatments, seedlings were grown for five days at 24oC before being transferred at dawn of the sixth day to 10oC and grown for seven additional days.
|
| Growth protocol |
Seeds were surface-sterilized in 50% bleach containing 0.01% Tween-20 and stratified for five days in 0.1% agarose in the dark at 4oC. Seeds were then sown onto sterile Whatman filter paper (Whatman, www.whatman.com) and placed on square plates containing 50 mL of MS medium at pH 5.8 with 0.8% type I micropropagation agar (Caisson Laboratories, www.caissonlabs.com). All seedlings were grown in Percival CU-30L2 growth chambers (Percival Scientific, www.percival-scientific.com), set to either constant 24oC or 10oC and identical long-day conditions (16 hr light:8 hr darkness) with cool white light at 100 μmol/m2/s.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the Qiagen RNeasy Kit and contaminating genomic DNA digested on column with the Qiagen RNase-free DNase Set according to the manufacturer’s protocol (Qiagen, www.qiagen.com/us/).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared using the 3' IVT PLUS Reagent Kit according to standard Affymetrix protocols from 250 ng total RNA
|
| |
|
| Hybridization protocol |
Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45oC on the Arabidopsis ATH1 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000 7G.
|
| Description |
Nd0_60.CEL
|
| Data processing |
The data were analyzed with R/Bioconductor and normalized using RMA. The trimmed mean target intensity of each array was set to 100.
|
| |
|
| Submission date |
Jun 12, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Bryan Thines |
| E-mail(s) |
[email protected]
|
| Phone |
253-879-3797
|
| Organization name |
University of Puget Sound
|
| Department |
Biology
|
| Street address |
1500 North Warner Street
|
| City |
Tacoma |
| State/province |
Washington |
| ZIP/Postal code |
98416 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE99947 |
Expression data from wild type (No-0) and fbs1-1 insertion line whole Arabidopsis seedlings in cold |
|
