|
| Status |
Public on Mar 04, 2014 |
| Title |
545060_A09_I317_circadien_B73_CRS_B73_0_cc24h |
| Sample type |
RNA |
| |
|
| Source name |
maize_B73_circadian cycle_24h_light
|
| Organism |
Zea mays subsp. mays |
| Characteristics |
genotype: standard maize line B73
phenotype: sampled after 24h in continuous light
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.
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| |
|
| 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 24h after lights on. It is the second 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.).
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| |
|
| 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 |
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