|
| Status |
Public on May 17, 2014 |
| Title |
Roots_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
P. hybrida leafy cutting_root system
|
| Organism |
Petunia x hybrida |
| Characteristics |
cultivar: Mitchell
tissue: Root
developmental stage: 24 days post excision of cuttings
|
| Growth protocol |
Leafy stem cuttings of Petunia hybrida cv. Mitchell were used for all experiments. Cuttings were produced on donor plants which were kept in short day condition with 10 hours light per day. All samples were collected at the same time of the day (2 h after the onset of light). Excised leafy cuttings harboring four to five leaves of similar size were placed in plastic trays with a size of 38×58 cm containing perlite (Perligran A, particle size 0-6 mm, Knauf Perlite GmbH, Dortmund, Germany). Perlite is an aluminium silicate, which has been expanded by heating to ca. 1000 °C. The substrate is chemically inert and does not contain mineral nutrients. Trays containing cuttings were watered and covered completely with a light-permeable top to maintain a humid environment. Cuttings were put in a phytotron and cultivated under the following growth conditions: temperature 20°C (night) and 22°C (day), humidity 60% (night) and 85% (day), time regime 10 h light and 14 h dark and a light intensity of 250 µmol x m-2 x s-1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from petunia cutting base as described by Logemann et al. (1987).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Switzerland, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Switzerland, following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Switzerland, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
To provide control tissues, petunia adventitious root system harvested 24 days post excision of cuttings (begin of lateral root formation) was used as fully developed root system. It is the third of four biological replicates used in this experiment.
|
| Data processing |
Data processing and normalization were performed by NimbleGen Systems Inc., Switzerland, following their standard operating protocol. See www.nimblegen.com.
Normalized expression values of different time points (0 hpe - 192 hpe) were compared with 0 hpe. Significantly up- or down-regulated genes were recognized via Rank Product (RP) analysis using MeV (MultiExperiment Viewer, version 4.4.1.) software. For each individual time point, the expression values of each replicate were divided by expression values of all four replicates at 0 hpe, followed by a log2-transformation for the Rank Product analysis (to generate M-values). Then, median values of these paired log-fold changes were calculated for each gene-related sequence identifier. Finally, the median values were back-transformed by a power of two in order to obtain the real expression ratios. The same procedure was carried out for the comparison of control tissues. To extract up or down-regulated genes, median ratios with values above two (>2) were determined as up-regulated and median ratios with values below 0.5 (<0.5) were determined as down-regulated. Putative genes showing expression value ratios more than 2 or less than 0.5 were considered as induced or repressed genes respectively (M-value > 1 or < 1). Based on the RP statistical analysis for each gene, using 1000 permutations, P-values below (≤0.01) were considered as significant differentially expressed. Cluster analyses (K-means clustering method) and preparation of expression graphs were performed using Genesis software version 1.7.6.
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| |
|
| Submission date |
May 16, 2014 |
| Last update date |
May 17, 2014 |
| Contact name |
Philipp Franken |
| E-mail(s) |
[email protected]
|
| Organization name |
Leibniz Institute of Vegetable and Ornamental Crops - IGZ EV
|
| Street address |
Theodor-Echtermeyer-Weg 1
|
| City |
Grossbeeren |
| ZIP/Postal code |
D-14979 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18705 |
| Series (1) |
| GSE57752 |
Gene expression analysis during adventitious root formation in petunia cuttings |
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