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Pipeline publication

[…] default settings to generate raw data, which were saved as CEL files. The raw data were normalized using a robust multichip analysis approach implemented in the Affy package [,]. Analysis of variance (ANOVA) was used to look for significant differences between samples, using transformation and wild type as factors. The probe sets were filtered for a 2-fold or greater change in expression in RB and SBT, then filtered for a 1.5-fold expression level difference in M. Differentially expressed genes were ranked by P values, and genes with a P value of ≤0.05 were considered differentially expressed at a statistically significant level. Gene annotation was carried out based on similarity scores in BLASTX comparisons against sequences contained in the Harvest: Citrus database (http://harvest.ucr.edu/). Differentially expressed genes were further analyzed using MapMan Bin (http://ppdb.tc.cornell.edu/default.aspx). The subcellular localization of differentially expressed peroxidase genes was predicted using TargetP (http://www.cbs.dtu.dk/services/TargetP/) and SUBA3 (http://suba.plantenergy.uwa.edu.au/). Peroxidase classification was based on PeroxiBase analysis (https://peroxibase.toulouse.inra.fr/tools/peroxiscan.php)., Starch contents in various calli (20-day-old) were detected by the anthrone reagent method according to Chen et al. []. The procedure of starch granules isolation was based on the method described by Ritte et al. [] with minor modifications. Five grams from each callus were mixed with 10 ml extraction buffer [100 mM N-2-hydroxyethylpiperazine-N-2-ethanesulfonic acid (HEPES)-KOH (pH 8.0), 1 mM ethylenediaminetetraacetic acid (EDTA), and 0.05% (v/v) Triton-X-100] and homogenized […]

Pipeline specifications

Software tools BLASTX, MapMan, TargetP