|
| Status |
Public on Sep 20, 2022 |
| Title |
wt2 |
| Sample type |
RNA |
| |
|
| Source name |
wt Control condition
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
tissue: leaves
expt condition: wt Control condition
|
| Treatment protocol |
Seedlings were incubated with 100uM cadmium for 30 minutes or 24 hours. Controls were incubated in a cadmium-free solution.
|
| Growth protocol |
Seedlings were grown for two weeks on solid MS medium, three independent biological replicates, each composed of at least five different seedlings, were used per experimental condition
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from seedlings by the acid guanidine thiocyanate–phenol–chloroform method using the Trizol reagent kit according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by the Functional Genomics Lab (Univ. Verona, IT) using NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by the Functional Genomics Lab (Univ. Verona, IT) using NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
Control condition
|
| Data processing |
Differential expression analysis has been performed with LIMMA (Linear Models Microarray Analysis; G. K. Smyth, 2005) R package and custom functions. Data preprocessing:background correction: normexp, quantile normalization, internal replicate summarization: median. Statistical analysis:linear models approach for the assessment of differential expression, P values were adjusted for multiplicity with BH method (Benjamini and Hochberg, 1995).
|
| |
|
| Submission date |
Mar 24, 2022 |
| Last update date |
Sep 20, 2022 |
| Contact name |
Laura Carmen Terron Camero |
| E-mail(s) |
lauteca@ipb.csic.es
|
| Phone |
658638526
|
| Organization name |
IPBLN
|
| Department |
Bioinformática
|
| Street address |
Avda. del Conocimiento 17. P. T. Ciencias de la Salud
|
| City |
Granada |
| State/province |
Granada |
| ZIP/Postal code |
18016 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13970 |
| Series (1) |
| GSE199325 |
Gene network downstream plant stress response modulated by peroxisomal H2O2 |
|
