|
| Status |
Public on May 01, 2011 |
| Title |
Sc WT 7 days cold |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Sc wild type experimental samples 7 days cold
|
| Organism |
Solanum commersonii |
| Characteristics |
genotype/variation: wild type
|
| Treatment protocol |
Three independent experiments were done for cold treatments. Eight hours after dawn, plants were transfered to 2oC with 50 mmol m-2s-1 light intensity, tissue was harvested after 2h, 24h and 7d of cold. Control plants were kept at 25oC and 350 mmol m-2s-1 light intensity and tissue was harvested after 2h and 24h. For the 35S::AtCBF3 transgenic lines, three independent Sc lines and 2 St lines were used, 8h after dawn tissue was harvested. Tissue was frozen into liquid nitrogen and store at -80oC
|
| Growth protocol |
Sc and St wild type plants and transgenic lines were grown for 3 weeks at 25oC and 350 mmol m-2s-1 light intensity on 16:8 photoperiod.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from leaf tissue using Rneasy Plant Mini Kits (Qiagen).
|
| Label |
Cy3,Cy5
|
| Label protocol |
20 mg of total RNA were reverse transcribed and labeled with Cy5 or Cy3 by the indirect aminoallyl method (http://www.jcvi.org/potato/sol_ma_protocols.shtml)
|
| |
|
| Channel 2 |
| Source name |
Sc wild type control samples 24h warm
|
| Organism |
Solanum commersonii |
| Characteristics |
genotype/variation: wild type
|
| Treatment protocol |
Three independent experiments were done for cold treatments. Eight hours after dawn, plants were transfered to 2oC with 50 mmol m-2s-1 light intensity, tissue was harvested after 2h, 24h and 7d of cold. Control plants were kept at 25oC and 350 mmol m-2s-1 light intensity and tissue was harvested after 2h and 24h. For the 35S::AtCBF3 transgenic lines, three independent Sc lines and 2 St lines were used, 8h after dawn tissue was harvested. Tissue was frozen into liquid nitrogen and store at -80oC
|
| Growth protocol |
Sc and St wild type plants and transgenic lines were grown for 3 weeks at 25oC and 350 mmol m-2s-1 light intensity on 16:8 photoperiod.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from leaf tissue using Rneasy Plant Mini Kits (Qiagen).
|
| Label |
Cy5,Cy3
|
| Label protocol |
20 mg of total RNA were reverse transcribed and labeled with Cy5 or Cy3 by the indirect aminoallyl method (http://www.jcvi.org/potato/sol_ma_protocols.shtml)
|
| |
|
| |
| Hybridization protocol |
The slides were hybridized using the indirectly labeled aminoallyl probes hybridization method (http://www.jcvi.org/potato/sol_ma_protocols.shtml)
|
| Scan protocol |
Slides were scaned using a Affymetrix 428 Array scanner.
|
| Description |
Sc C7d: 3 slides = 3 replicates
|
| Data processing |
Slide images were quantified using Genepix 3.0 (Axon Instruments, Union City, CA). GPR files were obtained. The data were normilized using the print tip loess method in the Limma package (Smyth 2004). A list of differentialy expressed clones were ranked based on p value, using false discovery rate to correct for multiple testing. Log2 ratios (M) were obtained from limma as average of the 3 biological replicates (with the exeption of St transgenic lines that were only 2). Then these Log2 ratios were averaged for the two clone technical replicates in each slide.
|
| |
|
| Submission date |
Jun 18, 2010 |
| Last update date |
May 01, 2011 |
| Contact name |
Marcela Carvallo |
| E-mail(s) |
carvall1@msu.edu
|
| Organization name |
Michigan State University
|
| Department |
Plant Research Laboratory
|
| Lab |
Michael Thomashow
|
| Street address |
310 Plant Biology bldg
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL10564 |
| Series (1) |
| GSE22449 |
Transcriptomes profile of Solanum tuberosum (St) and Solanum commersonii (Sc) under cold stress and AtCBF3 overexpression. |
|
