|
| Status |
Public on Nov 18, 2009 |
| Title |
Wang_1-4_WT-Col-250-micromolar-K-nitrate-20-min-roots_Rep2_ATH1 |
| Sample type |
RNA |
| |
|
| Source name |
Col-0
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: Col-0
developmental stage: 10 days
tissue: Roots
|
| Growth protocol |
Arabidopsis ecotype Columbia was grown at 25°C to 27°C under constant illumination with agitation at 120 rpm for 10 d. Plants were grown in a 50-mL glass beaker containing a segment (20 mM in height) of a 50-mL Falcon centrifuge tube with triangular openings at bottom to allow for liquid flow. On top of the tube was a disc of polypropylene mesh (250-micron pore size, 25 mM in diameter). Beakers initially contained 25 mL of sterile medium (described above) and approximately 50 surface-sterilized seeds evenly distributed on the mesh disc. On d 5, 5 mL of medium was removed from the beaker to allow shoots to stay above the medium liquid. The beaker top was covered with three layers of aluminum foil to keep the culture sterile.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy kit protocol
|
| Label |
biotin
|
| Label protocol |
Labelled using protocol described in Affymetrix manual "3' IVT Express Kit User Manual"
|
| |
|
| Hybridization protocol |
Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA
|
| Scan protocol |
Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.
|
| Description |
Seeds were treated with 30% Commercial bleach, 0.05% Triton X-100 for 10 min at room temperature and washed with sterile water 5 times in the hood. Individual component stock autoclaved separately; FeEDTA filter-sterilized
|
| Data processing |
Raw data from the microarrays was normalized at probe-level using MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system
|
| |
|
| Submission date |
Nov 12, 2009 |
| Last update date |
Nov 17, 2009 |
| Contact name |
Nottingham Arabidopsis Stock Centre (NASC) |
| E-mail(s) |
[email protected]
|
| Phone |
+44 (0)115 951 3237
|
| Fax |
+44 (0)115 951 3297
|
| URL |
http://arabidopsis.info/
|
| Organization name |
Nottingham Arabidopsis Stock Centre (NASC)
|
| Department |
School of Biosciences, University of Nottingham
|
| Street address |
Sutton Bonington Campus
|
| City |
Loughborough |
| ZIP/Postal code |
LE12 5RD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE18984 |
Treatment of Arabidopsis with low concentration of nitrate |
|
