az-specific microarray chip  (Genotypic Technology Pvt Ltd)

Journal: Frontiers in Plant Science

Article Title: Examination of the Abscission-Associated Transcriptomes for Soybean, Tomato, and Arabidopsis Highlights the Conserved Biosynthesis of an Extensible Extracellular Matrix and Boundary Layer

doi: 10.3389/fpls.2015.01109

Figure Lengend Snippet: Overall perspective on major changes in gene expression during abscission of soybean leaves, tomato flowers and Arabidopsis floral organs . (A) The percent of soybean pulvinar leaf abscission and the percent of genes with greater than 8-fold change (log2 >3 or < −3) in expression relative to the total number of genes expressed (37,572) and the differential expression of the same genes relative to the average total RPKM for each RNA sample (666,213 RPKM). (B) Similar to (A) except that tomato flower abscission had 26,572 expressed genes with a total average microarray signal of 64,696,620. (C) The percent of expressed genes in wild-type Arabidopsis receptacles relative to genes in the double mutant hae-hsl2 and the differential expression of the same genes (Niederhuth et al., ). In the Arabidopsis data, 20,883 genes were counted as expressed with a total mean of 38,770,114 reads. Because differential expression was much less in the Arabidopsis data, 2-, 4-, and 8-fold differences are plotted as a bar graph.

Article Snippet: The Meir lab at the Volcani Center, Bet-Dagan, Israel has prepared a tomato AZ-specific microarray chip in collaboration with Genotypic Technology Pvt.

Techniques: Gene Expression, Expressing, Quantitative Proteomics, Microarray, Mutagenesis

Journal: Frontiers in Plant Science

Article Title: Examination of the Abscission-Associated Transcriptomes for Soybean, Tomato, and Arabidopsis Highlights the Conserved Biosynthesis of an Extensible Extracellular Matrix and Boundary Layer

doi: 10.3389/fpls.2015.01109

Figure Lengend Snippet: Line graphs (soybean and tomato) and volcano plots (Arabidopsis) showing the change in gene expression for selected groupings of genes and some individual genes . The percent of abscission is indicated in the graph at the top left corner the sections for (A) soybean and (B) tomato as a reference. (A) The Y-axes indicate the percent expression relative to total RPKM for all 37,572 expressed soybean genes (transcriptome). The X-axes indicate the length of exposure to ethylene. Solid circles represent expression in the LAZ and the open triangles in petioles (NAZ-pet). (B) Similar to (A) but The Y-axes indicate the percent expression relative to total microarray signal for 26,527 expressed tomato genes. The X-axes indicate the hours after removal of the flowers, auxin source. Solid circles represent expression in the FAZ and the open triangles in NAZ. The number within the parenthesis to the right of each category or gene name is the number of genes included for that particular graph. Plots with an L2>3 after the number in parentheses show the cumulative expression for only those genes with a significant 8-fold increase in expression ( p < 0.015 and log2>3 for any time relative to 0 h). Standard error bars cannot be calculated for plots of multiple genes. (C) Volcano plots of differential expression in WT/ hae-hsl2 receptacles at developmental stage 15. Y-axes are the −log10 of the p -values. A p < 1% (<0.015) is a p -value of −log10 >2, which is indicated by the horizontal line through the middle. Any expression with a p -value (significance) of less than 0.0001 (−log10>4) was set to a minimum of 0.0001, which is why many points align across the top. The X-axes are the log2 ratios for expression (reads) of WT/ hae-hsl2 . The genes in each category, their nomenclature, log2 ratios, and annotations are given in Supplemental Files – for soybean, tomato, and Arabidopsis, respectively.

Article Snippet: The Meir lab at the Volcani Center, Bet-Dagan, Israel has prepared a tomato AZ-specific microarray chip in collaboration with Genotypic Technology Pvt.

Techniques: Gene Expression, Expressing, Microarray, Quantitative Proteomics