|
| Status |
Public on Apr 01, 2011 |
| Title |
leaf 30%Inhibition rep4 [Populus] |
| Sample type |
RNA |
| |
|
| Source name |
Populus trichocarpa leaf, 30% inhibition
|
| Organism |
Populus trichocarpa |
| Characteristics |
tissue: leaf, first fully expanded
line: 93968
treatment: Photosynthesis at 30% inhibition from optimum
|
| Treatment protocol |
For the microarray analysis, fully expanded leaf samples from 4 randomly collected plants per species were harvested at 4 physiological states as determined from prior gas exchange measurements (growth temperature - baseline, photosynthetic optimum, 20% inhibition of optimum and 30% inhibition of optimum). The temperature response curves were created by increasing temperature step-wise (2 °C per 10 mins) from 22 to 42 °C to the desired physiological state and waiting 20-30 mins for photosynthesis to stabilize before sampling. Each curve took 3-4 h to complete.
|
| Growth protocol |
Dormant cuttings of black cottonwood (Populus trichocarpa clone 93-968) averaging ~0.5 cm diameter, 25 cm length, and 2-3 buds were rooted using 0.3% IBA and grown in a Conviron BDW80 walk-in growth chamber at 22 °C, 60% relative humidity, a 18 h photoperiod, and 350 μmol m-2s-1 light intensity. Plants were watered as needed and fertilized weekly according 250 ppm N using Jack's professional.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was converted to ds cDNA using a SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp) according to the protocol provided by Roche for NimbleGen high-density microarrays.
|
| Label |
biotin
|
| Label protocol |
RNase A cleanup, cDNA precipitation and sample labeling were carried out according Roche provided protocol
|
| |
|
| Hybridization protocol |
Hybridization was performed according to Roche protocols
|
| Scan protocol |
Dried slides were scanned using an Agilent Scanner (Agilent Technologies, Santa Clara, CA) with a PMT gain of 100% at 5 µm resolution.
|
| Description |
Gene expression data from the first fully expanded leaf of Populus trichocarpa at 30% inhibition from optimum
|
| Data processing |
Images of all scanned slides were aligned using NimbleScan version 2.5 and pair reports were created using the slide design file provided by Roche NimbleGen. An annotation package for this array was created using the pdInfoBuilder (v.2.4) Bioconductor open access package run in the R statistical framework (R Development Core Team, 2007).
|
| |
|
| Submission date |
Dec 20, 2010 |
| Last update date |
Apr 01, 2011 |
| Contact name |
David J Weston |
| E-mail(s) |
westondj@ornl.gov
|
| Phone |
865 241-8323
|
| Fax |
865 576-9939
|
| Organization name |
David Weston
|
| Department |
Environmental Sciences Division
|
| Street address |
Bldg. 1062 Rm. 210
|
| City |
Oak Ridge |
| State/province |
TN |
| ZIP/Postal code |
37830 |
| Country |
USA |
| |
|
| Platform ID |
GPL11341 |
| Series (2) |
| GSE26195 |
Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max [Populus] |
| GSE26199 |
Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max |
|
