|
| Status |
Public on Mar 04, 2014 |
| Title |
544647_A11_I309_circadien_B73_CRS_B73_0_nuit |
| Sample type |
RNA |
| |
|
| Source name |
maize_B73_circadian cycle_predawn
|
| Organism |
Zea mays subsp. mays |
| Characteristics |
genotype: standard maize line B73
phenotype: sampled at predawn
tissue: leaf elongation zone
|
| Growth protocol |
Well watered plants of the maize line B73 were previously grown (entrainement period) with 12h of photoperiod and with high day/night variations of evaporative demand in controlled conditions (day: 28°C, vapour pressure deficit of 3kPa and light 600µmol m-2 s-1; night: 20°C, vapour pressure deficit of 0.8kPa and darkness).
Leaf samples were collected at predawn (1h before lights on) and 12 and 24 hours in continuous light after light switched on.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with NanoDrop.
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed using One-Color DNA Labeling 5223555001 kit, Roche NimbleGen Inc. following the standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed using Nimblegen Hybridization system following the standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed with scanner MS200 Roche-NimbleGen with autogain mode, following the standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample of leaf elongation zone was collected from maize plants during the predawn. It is the first of three biological replicates used in this experiment, each from separate plants.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249)and quantile normalization (Bolstad et al. Bioinformatics 19(2):185) as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
Mar 03, 2014 |
| Last update date |
Mar 04, 2014 |
| Contact name |
Cecilio Frois Caldeira |
| E-mail(s) |
cecilio.frois@gmail.com
|
| Organization name |
INRA - Institut National de la Recherche Agronomique
|
| Department |
Herault
|
| Lab |
LEPSE
|
| Street address |
2 place Viala
|
| City |
Montpellier |
| ZIP/Postal code |
34060 |
| Country |
France |
| |
|
| Platform ID |
GPL18328 |
| Series (1) |
| GSE55524 |
Expression analysis of maize (Zea mays L.) genes in continuous light |
|
