|
| Status |
Public on Jul 31, 2013 |
| Title |
20_DAP_20C_Rep2 |
| Sample type |
RNA |
| |
|
| Source name |
20_DAP_Cy5
|
| Organism |
Medicago truncatula |
| Characteristics |
tissue: seed
genetic background: A17
developmental stage: 20_DAP maturation
phenotype: Wild-type
treatment: Seeds developed at 21-19°C 16h
age: 20 days after flowering
harvest date: 06/06/12
|
| Treatment protocol |
Medicago truncatula seeds developed at 16h, 19-21°C from 1 DAP to DS stage
|
| Growth protocol |
Five Medicago truncatula plants were grown at controlled light/temperature conditions: 16h, 19-21°C from the stage of flowering to the end of seed maturation. Seeds were collected at different maturation stages, from 8 day after pollination (DAP) to Abscission. Dry seeds (DS) was the last analysed stage of development, after abscission seeds were let in the same environmental conditions for one week.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each data point of seed development and for each repetition, 50 seeds were collected and the total RNA was extracted with Macherey-Nagel's Nucleospin Plant II Kit according manufacturer's recommendations
|
| Label |
Cy5
|
| Label protocol |
400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse_transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine_3 (Cy3) or Cyanine_5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean_up column kits (Macherey_Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND_1000 (Nanodrop Technologies, DE, USA). Labelled samples (30 pmol) were combined and co_hybridized to the Medtr_v1 12x135K arrays.
|
| |
|
| Hybridization protocol |
Hybridization was performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnight. Slides were washed and dried prior to scanning.
|
| Scan protocol |
Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche_NimbleGen MS200. DEVA Software v1.2.1 was used to extract pair_data files from the scanned images.
|
| Data processing |
All statistical analyses on the gene expression data were performed using R language, version 2.5.1 (R Development Core Team, 2011) and LIMMA package (Smyth G.K., 2005) from the Bioconductor project. For the processing steps, data were normalized by the lowess method in LIMMA.
|
| |
|
| Submission date |
Jul 30, 2013 |
| Last update date |
Jul 31, 2013 |
| Contact name |
Sandra Pelletier |
| E-mail(s) |
[email protected]
|
| Organization name |
INRA
|
| Lab |
IRHS
|
| Street address |
42, rue Georges Morel - BP 60057
|
| City |
BEAUCOUZE |
| ZIP/Postal code |
49045 |
| Country |
France |
| |
|
| Platform ID |
GPL16373 |
| Series (2) |
| GSE49350 |
Medicago truncatula seed development at 21-19°C |
| GSE53526 |
Medicago truncatula seed development under different growth conditions |
|
