germplasm name: Ofanto organism part: Leaf cell type: all_leaf_cells development stage: 3 leaf fully expanded ('PO:0001053') growth media: field soil
Extracted molecule
total RNA
Extraction protocol
Hot Phenol/Guanidine Thiocyanate and RNeasy Clean up
Label
biotin
Label protocol
Affy- Whole transcript target preparation
Hybridization protocol
Affy-Oven320
Scan protocol
Affy- Array Scanning
Description
Plants were grown in a growth chamber under conditions miming the natural growing season in the field. Germination was carried out at 6°C in complete darkness until the shoot came out, then the growth conditions were set at 10 hrs light and 14 hrs dark at 8°C and 6°C, respectively, relative humidity 60%. Growing condition were then modified according to the plants growth stage: 13 hrs light and 11 hrs dark at 12°C and 8°C, respectively, relative humidity 50% at second leaf stage; 14 hrs light and 10 hrs dark at 15°C and 10°C, respectively, relative humidity 50%, at the third leaf stage; 15 hrs light and 9 hrs dark at 15°C and 12°C, respectively, relative humidity 50%, at tillering stage; 15 hrs light and 9 hrs dark at 19°C and 15°C, respectively, relative humidity 40% at booting stage. Light was provided by 400-W high-pressure lamps (Philips) with a photon flux density of 500 mmol m-2 s-1. The plants were grown in pots (0.38 length x 0.16 width x 0.14 m height) filled with a substrate of soil (clay-loam), sand and peat in a 6:3:1 ratio. The pots filled with the substrate were standardized for the weight and Field Capacity (FC), and the dried weight (DW) were measured. A complete randomized block design with three replications was adopted. The plantlet number was standardized at 12 seeds/pot. Ammonium biphosphate (pre-sowing) and ammonium nitrate (shoot emergence and tillering) were used as fertilizers for a total amount equivalent to 60 kg/ha of P and 150 kg/ha of N. Powdery mildew was controlled with fungicide treatment (Folicur 1.5 g/l) from tillering onwards. The irrigation was made with tap water (0.5 dS m-1), weighing pots and intervening whenever the soil lost 50% of available water, bringing it back to a soil water content (SWC) corresponding to 28% of FC. DS was imposed by withholding water and allowing the pots to reach a SWC equal to 12.5% of FC, other growing conditions were as in control plants. To monitor the SWC the pots weight was measured twice per day. The flag leaves detached at mid-point of the light period were collected for transcriptomic analysis three days after the imposition of stress (May still include original submitter created erros/discrepancies)
Data processing
The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.
Submission date
Mar 27, 2013
Last update date
Mar 22, 2016
Contact name
PLEXdb Curator, Sudhansu Dash
Organization name
Iowa State University
Department
Virtual Reality Application Center
Lab
PLEXdb
Street address
1023 Crop Genomes Informatics Lab (Iowa State University)
