|
| Status |
Public on Sep 12, 2018 |
| Title |
256449110007_b3 - 9_C15_V2 vs 11_C20_V2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
11_C20_V2
|
| Organism |
Zea mays |
| Characteristics |
days after pollination: 20
tissue: vitreous endosperm
line: flint maize
harvest date: 21-08-14
|
| Treatment protocol |
no treatment
|
| Growth protocol |
seed - outdoor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
11_C20_V2:100mg. (Qiagen_RNeasy.pdf)
|
| Label |
Cy5
|
| Label protocol |
labelling Cy3 and Cy5 direct, amplification=yes, total RNA .
|
| |
|
| Channel 2 |
| Source name |
9_C15_V2
|
| Organism |
Zea mays |
| Characteristics |
days after pollination: 15
tissue: vitreous endosperm
line: flint maize
harvest date: 14-08-14
|
| Treatment protocol |
no treatment
|
| Growth protocol |
seed - outdoor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
9_C15_V2:100mg. (Qiagen_RNeasy.pdf)
|
| Label |
Cy3
|
| Label protocol |
labelling Cy3 and Cy5 direct, amplification=yes, total RNA .
|
| |
|
| |
| Hybridization protocol |
11_C20_V2 Cy5 / 9_C15_V2 Cy3 : 20pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.
|
| Scan protocol |
GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 50%, Cy5:635nm,pmt voltage 700V,laser power 45%
|
| Description |
Delineation of the metabolic pathways involved in maize endosperm vitreousness.
|
| Data processing |
For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.
|
| |
|
| Submission date |
Sep 05, 2018 |
| Last update date |
Sep 12, 2018 |
| Contact name |
Stéphanie Pateyron |
| E-mail(s) |
pateyron@evry.inra.fr
|
| Organization name |
IPS2_Institute of Plant Sciences Paris-Saclay
|
| Lab |
Transcriptomic Plateforme POPS
|
| Street address |
Rue de Noetzlin _ Batiment 630
|
| City |
Orsay |
| ZIP/Postal code |
91405 |
| Country |
France |
| |
|
| Platform ID |
GPL22405 |
| Series (1) |
| GSE119550 |
cinetique comparison-FUI GranoFlakes. |
|
