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E-GEOD-10857 - Transcription profiling of rice root tips before, at and buckled by a hard layer in two rice varieties

Status
Submitted on 17 March 2008, released on 6 November 2008, last updated on 10 June 2011
Organism
Oryza sativa
Samples (12)
Array (1)
Protocols (6)
Description
The aim of this study was to determine the changes in gene expression of rice root tips when they came in to contact with a hard layer (60% wax layer). Three categories of root tips were sampled; tips before the hard layer, tips that had come into contact with the hard layer and root tips which had buckled after coming into contact with the hard layer. Two genotypes (Azucena and Bala) that vary in there ability to penetrate a hard layer were selected for a genotype comparison of gene expression at the hard layer. Experiment Overall Design: A chamber with the internal dimensions of 10 x 5 x 25cm consisting of a glass back, Perspex front and aluminium spacers with an open bottom and top was set at an angle of 15o in a large sand filled tray and filled up to 19.5 cm with dry sand. The sand was watered with nutrient solution, the sand was levelled and then a 5mm thick 60% wax layer (prepared using a ratio of 3:2 (w/w) of pastillated paraffin wax / white soft wax) was poured on the sand. Once the wax layer had set, two small holes were placed at the back of the wax layer to allow water drainage and water exchange via capillary action. The chamber was then filled up with more dry sand, and then watered using nutrient solution. Nutrient solution was then added to the large tray which the chamber had been placed; this was regularly topped up and allowed the watering of the chamber by capillary action. Light was eliminated from the chambers using white (exterior face)/black (interior face) plastic sheeting. Experiment Overall Design: Azucena and Bala seeds were surface sterilized with 1% (v/w) sodium hypochlorate for 5 minutes, then rinsed thoroughly three times with water and then germinated on moist tissue paper for 48 hours at 37oC. A single germinated seed was then sown 1 cm below the surface of the sand in each chamber. Experiment Overall Design: The plants were grown in a controlled environment room with a 12 hour day and night, with a day temperature of 30oC and a night temperature of 24oC with 300 µmol m-2 s-1 PAR. After 24 days the chamber was dismantled and the root tips of 5 mm length were harvested from Azucena plants for subsequent RNA extractions from the three categories as follows; a) roots which were between 5-10 mm above the wax layer; b) roots at the wax layer; c) roots which had buckled at the wax layer and grown 7-10 mm after buckling. From Bala plants, only root tips at the layer were harvested. Experiment Overall Design: Each condition was indsependently replicated 3 times.
Experiment types
transcription profiling by array, unknown experiment type
Contact
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-10857.idf.txt
Sample and data relationshipE-GEOD-10857.sdrf.txt
Raw data (1)E-GEOD-10857.raw.1.zip
Processed data (1)E-GEOD-10857.processed.1.zip
Experiment designE-GEOD-10857.biosamples.png, E-GEOD-10857.biosamples.svg
Array designA-AFFY-126.adf.txt
R ExpressionSetE-GEOD-10857.eSet.r
Links