|
| Status |
Public on Jan 31, 2012 |
| Title |
leaf_LLN_NLN_rep1_ds1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
leaf, low light, Nadro
|
| Organism |
Triticum aestivum |
| Characteristics |
variety: Nadro
tissue: leaf
light condition: low light
|
| Growth protocol |
Seeds of wheat plants (Triticum aestivum L.) winter varieties Mv Emese, with a high level of freezing tolerance, and spring variety Nadro, with a low level of freezing tolerance, were sown in loamy soil and sand, 3:1 (v:v). The plants were grown for 10 d in a Conviron PGR 15 growth chamber with a 16 h/8 h light/dark period, at 20/18°C (day/night) with 75% relative humidity and 250 mmol m-2 s-1 (control, normal light) photosynthetic photon flux density (PPFD) at the leaf level, provided by metal halide lamps. Low temperature hardening was carried out in a chamber of the same type at a constant 5°C either under the light conditions of normal growth (light-hardened plants) or at 20 mmol m-2 s-1 PPFD (low light-hardened plants).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Two biological replicates with four technical replicates (each replicate consisted of five plants) were harvested. RNA was isolated using TRIzol reagent (Invitrogen) and the samples were DNase I treated and cleaned up with MinElute Kit (Qiagen) according to the manufacturer’s instructions. The RNA Integrity Number (RIN) of the samples was determined using the Agilent BioAnalyzer, and, equal amounts of RNA from the four technical replicates were pooled and used for cRNA amplification.
|
| Label |
Cy3
|
| Label protocol |
The RNA amplification and labeling procedure was done according to the manufacturer’s recommendations (Agilent).
|
| |
|
| Channel 2 |
| Source name |
leaf, normal light, Nadro
|
| Organism |
Triticum aestivum |
| Characteristics |
variety: Nadro
light condition: normal light
tissue: leaf
|
| Growth protocol |
Seeds of wheat plants (Triticum aestivum L.) winter varieties Mv Emese, with a high level of freezing tolerance, and spring variety Nadro, with a low level of freezing tolerance, were sown in loamy soil and sand, 3:1 (v:v). The plants were grown for 10 d in a Conviron PGR 15 growth chamber with a 16 h/8 h light/dark period, at 20/18°C (day/night) with 75% relative humidity and 250 mmol m-2 s-1 (control, normal light) photosynthetic photon flux density (PPFD) at the leaf level, provided by metal halide lamps. Low temperature hardening was carried out in a chamber of the same type at a constant 5°C either under the light conditions of normal growth (light-hardened plants) or at 20 mmol m-2 s-1 PPFD (low light-hardened plants).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Two biological replicates with four technical replicates (each replicate consisted of five plants) were harvested. RNA was isolated using TRIzol reagent (Invitrogen) and the samples were DNase I treated and cleaned up with MinElute Kit (Qiagen) according to the manufacturer’s instructions. The RNA Integrity Number (RIN) of the samples was determined using the Agilent BioAnalyzer, and, equal amounts of RNA from the four technical replicates were pooled and used for cRNA amplification.
|
| Label |
Cy5
|
| Label protocol |
The RNA amplification and labeling procedure was done according to the manufacturer’s recommendations (Agilent).
|
| |
|
| |
| Hybridization protocol |
The cRNA of two biological replicates labeled with Cy3 or Cy5 (dye-swap) were hybridized to the Agilent 4X44K Wheat Chip. The chip contains 43603 unique oligos, besides the positive and negative controls. The cRNA samples of Emese (E) and Nadro (N) plants grown at 18°C under normal (NL) and low (LL) light fluences were compared to each other in a simple loop design and E-NL vs. E-LL; N-NL vs. N-LL; E-NL vs. NLL and E-LL vs. N-LL comparisons were made.
|
| Scan protocol |
Scanning was performed, using an Agilent High-Resolution Microarray Scanner. The detection of signal intensities and the grid adjustment were accomplished with the Agilent Feature Extraction Software.
|
| Description |
DN-LN-rep1-ds1
rep1_ds1_015_04_SN_vs_FN_v2.txt
|
| Data processing |
Intensity data were imported into the R 2.10.0 statistical programming language. Further analysis was carried out using the LIMMA package of BIOCONDUCTOR. Background correction was done using the normexp method. Normalization of data within arrays was done using the loess method, and to normalize the data between arrays, the quantile method was used.
|
| |
|
| Submission date |
May 31, 2011 |
| Last update date |
Jan 31, 2012 |
| Contact name |
Endre Sebestyén |
| Organization name |
Semmelweis University
|
| Department |
1st Department of Pathology and Experimental Cancer Research
|
| Street address |
Üllői út 26.
|
| City |
Budapest |
| ZIP/Postal code |
1085 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL13627 |
| Series (1) |
| GSE29640 |
Light effect on the hormonal and transcriptional status of winter and spring wheat plants during cold hardening |
|
