|
| Status |
Public on Jul 04, 2017 |
| Title |
549626A04 - SXB139_3 vs SXB139_2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
SXB139_2
|
| Organism |
Triticum aestivum |
| Characteristics |
triticum aestivum (serix babax rils) - dev.stage (boyes et al. plant cell 2001): 0°cd
|
| Treatment protocol |
Name:Heat-treated - environmental treatment - temperature,temperature:time 250day . 250°Cd, see Table “RNA extracted”
|
| Growth protocol |
seed - Plants were grown under semi-controlled conditions in containers 2m2 and 0.5 m deep each, covered by transparent enclosures under natural light. Water was daily supplied but the water statute of the plants was not measured. The mean temperature of one container was set at 19°C and corresponded to the control samples. The mean temperature of a second container was set at 27°C and corresponded to the heat-treated samples. The elevated temperature was applied at Anthesis and lasted for 15 days after anthesis (15DAA), then it was lowered back to 19°C as for the control samples. To obtain a mean temperature of 19 °C on a daily basis, the temperature of the container was set at 21°C between 6am30 and 10pm30 and 15°C otherwise. To obtain a mean temperature of 27°C during the lag-phase, the containers were maintained at 29°C from 6am30 to 10pm30 and 23°C for the rest.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SXB139_2:55.3ug. (GDEC-extraction_protocol_of_total_RNA_from_wheat_grain.docx)
|
| Label |
Cy5
|
| Label protocol |
labelling Cy3 and Cy5 direct, amplification=yes, total RNA . (PT-SIGMA-01_30-10-2012_T.pdf)
|
| |
|
| Channel 2 |
| Source name |
SXB139_3
|
| Organism |
Triticum aestivum |
| Characteristics |
triticum aestivum (serix babax rils) - dev.stage (boyes et al. plant cell 2001): 0°cd
|
| Treatment protocol |
no treatment
|
| Growth protocol |
seed - Plants were grown under semi-controlled conditions in containers 2m2 and 0.5 m deep each, covered by transparent enclosures under natural light. Water was daily supplied but the water statute of the plants was not measured. The mean temperature of one container was set at 19°C and corresponded to the control samples. The mean temperature of a second container was set at 27°C and corresponded to the heat-treated samples. The elevated temperature was applied at Anthesis and lasted for 15 days after anthesis (15DAA), then it was lowered back to 19°C as for the control samples. To obtain a mean temperature of 19 °C on a daily basis, the temperature of the container was set at 21°C between 6am30 and 10pm30 and 15°C otherwise. To obtain a mean temperature of 27°C during the lag-phase, the containers were maintained at 29°C from 6am30 to 10pm30 and 23°C for the rest.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SXB139_3:74.2ug. (GDEC-extraction_protocol_of_total_RNA_from_wheat_grain.docx)
|
| Label |
Cy3
|
| Label protocol |
labelling Cy3 and Cy5 direct, amplification=yes, total RNA . (PT-SIGMA-01_30-10-2012_T.pdf)
|
| |
|
| |
| Hybridization protocol |
SXB139_2 Cy5 / SXB139_3 Cy3 : 30pmol. (Hyb_Scan_Nimb_GEO.doc)
|
| Scan protocol |
Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%
|
| Description |
The objective is to better understand the adaptive response of the wheat plant to an elevated mean temperature. Besides the morphological and ecophysiological responses, the changes in the expression of genes are investigated. Two genotypes (SxB49 and SxB139) are subjected to two different temperature regimes during the lag-phase of the developing grains. The profiling of the accumulation of gene transcripts throughout 12 developmental stages is carried out using a custom-designed 12x135K Roche NimbleGen gene expression microarray comprising the most recent NCBI wheat contig assembly and annotation (about 45 000 unigenes). This should permit both the identification of differentially expressed genes after heat treatment and the comparison of the behaviours of two wheat genotypes (SxB139 and SxB49).
|
| 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 |
Jun 29, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Soubigou-Taconnat Ludivine |
| E-mail(s) |
soubigou@evry.inra.fr
|
| Organization name |
INRA
|
| Department |
URGV
|
| Lab |
ADT
|
| Street address |
2 rue gaston crémieux
|
| City |
evry |
| ZIP/Postal code |
91000 |
| Country |
France |
| |
|
| Platform ID |
GPL23639 |
| Series (1) |
| GSE100642 |
12plex-wheat_2012-05-The wheat grain transcriptome response to high temperature |
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