|
| Status |
Public on Apr 01, 2016 |
| Title |
root_dark_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Drak grown roots
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
growth condition: in darksness
tissue: roots
|
| Treatment protocol |
Control: seedlings were grown with the shoot and root in presence of white light (75 umoles/m2 seg). Treatment: seedlings were grown with the shoot in presence of white light (75 umoles/m2 seg) but the roots in darksness.
|
| Growth protocol |
Arabidopsis seedlings were grown in half strench MS medium for 12 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from roots using the Trizol (Lifetechnologies) following the company procedure. This isolated RNA was then purified using the Quiagen RNA isolation kit.
|
| Label |
Cy3
|
| Label protocol |
cDNA was generated with 10 μg RNA using the double-stranded cDNA synthesis kit (Invitrogen), and cDNA was Cy3-labeled with the NimbleGen one-color DNA labeling kit (Roche).
|
| |
|
| Hybridization protocol |
Each microarray was hybridized with the NimbleGen hybridization kit, washed using the NimbleGen wash buffer kit (both from Roche)
|
| Scan protocol |
Microarrays were scanned at 2-μm double-pass at 16-bit resolution
|
| Description |
SAMPLE 2
This sample is of roots grown in darkness. It is the second of three biological replicates used in this experiment, each from independent in vitro cultured plates.
|
| Data processing |
Data were analyzed through robust multiarray analysis with NimbleGen Scan software v.2.60 (Roche).
Differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (Limma). P values were corrected for multiple testing using the Benjamini-Hochberg method (false discovery rate) (Reiner et al., 2003).
|
| |
|
| Submission date |
Apr 21, 2015 |
| Last update date |
Apr 01, 2016 |
| Contact name |
Juan Carlos del Pozo |
| E-mail(s) |
pozo@inia.es
|
| Organization name |
Centro de Biotecnología y Genómica de Plantas
|
| Department |
Biotechnology
|
| Lab |
180
|
| Street address |
Campus de Montegancedo, UPM
|
| City |
Pozuelo de Alracon |
| State/province |
Madrid |
| ZIP/Postal code |
28223 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13970 |
| Series (1) |
| GSE68093 |
Root development and responses are alerted by light |
|
