|
| Status |
Public on Dec 06, 2016 |
| Title |
mock treatment of 35S-PLT4-GR, biological rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
whole seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype/variation: 35S-PLT4-GR
tissue: whole seedlings
treatment: mock
treatment time: 6 hrs
|
| Treatment protocol |
The next day, dex was added to each of the flasks to a final concentration of 10 µM except the mock samples to which an equal amount of DMSO was added. Each genotype was induced with 5 minute intervals which meant that all samples were harvested within half an hour to minimize the effect of time of day on the resulting transcriptome. After 6 hour induction seedlings were quickly harvested through a sieve, transferred briefly onto liquid absorbing paper and flash frozen in liquid nitrogen. In a separate experiment 35S::PLT2-GR seedlings were treated as described above with dex and, as a mock control, DMSO.
|
| Growth protocol |
35S::PLT[1,3,4,5,7]-GR seedlings were germinated on 0.5x GM agar and four day old seedlings of each genotype were subsequently divided in 3 batches (representing three biological replicates) of ~50 seedlings into 50 ml liquid 0.5x GM in erlenmeyer flasks. We chose the 35S::PLT4-GR line to be used as mock sample and for this line an additional 3 erlenmeyer flasks were prepared. Seedlings were cultured overnight under mild shaking (~75 rpm).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from the seedlings using the Spectrum Plant Total RNA kit (Sigma-Aldrich) and used for microarray hybridisation.
|
| Label |
biotin
|
| Label protocol |
Outsourced at ServiceXS (Leiden, the Netherlands)
|
| |
|
| Hybridization protocol |
Outsourced at ServiceXS (Leiden, the Netherlands)
|
| Scan protocol |
Outsourced at ServiceXS (Leiden, the Netherlands)
|
| Description |
Gene expression data from whole seedlings for the control
|
| Data processing |
Analysis with R/Bioconductor. Arrays were RMA normalized and differential gene expression analysis was performed with the limma package version 3.24.15
|
| |
|
| Submission date |
Mar 31, 2016 |
| Last update date |
Dec 06, 2016 |
| Contact name |
Luca Santuari |
| Organization name |
Wageningen University
|
| Department |
Plant Sciences Group
|
| Lab |
Plant Developmental Biology
|
| Street address |
Droevendaalsesteeg 1
|
| City |
Wageningen |
| ZIP/Postal code |
6708PB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL21674 |
| Series (2) |
| GSE79753 |
Induction of PLT1, PLT3, PLT4, PLT5 and PLT7 in whole seedlings |
| GSE79755 |
The PLETHORA gene regulatory network guides growth and cell differentiation in Arabidopsis roots |
|
