scanarray5000  (Packard Instruments)

Journal: The Plant Cell

Article Title: Integrative Transcript and Metabolite Analysis of Nutritionally Enhanced DE-ETIOLATED1 Downregulated Tomato Fruit ^[W]

doi: 10.1105/tpc.110.073866

Figure Lengend Snippet: Transcriptional Misregulation Resulting from DET1 Downregulation. The stages of fruit development at which the analysis were performed are indicated by MG (mature green), BR (breaker), and RR (red ripe). (A) Boxplots for log2 ratio (transgenic versus T56) of microarray expression data. P119 is shown in red and TFM7 in blue. Boxes show center quartiles (middle 50% of the data, whiskers extend to the most extreme data points that are no more than 1.5 times the interquartile range). The outliers are shown as filled circles. (B) Frequency distribution of expression values for P119 (red) and TFM7 (blue) across all developmental and ripening stages. The x axis represents log2 expression ratio of the DET1 variety versus T56 (control), indicating the relative changes in transcripts occurring within the data sets. The y axis shows the percentage of transcripts with a given relative expression value. An overwhelming proportion of expression values are above the T56 control level for P119, but TFM7 shows significant downregulation. (C) and (D) SOMs for TFM7 (C) and P119 (D). In each partition, the pattern reflects a general trend of expression gradient of the group across three developmental stages with vertical bars showing the variance in the group at each stage. A gene is assigned to a single partition with similar groups placed in nearby partitions. (E) and (F) Heat maps of the gene expression data for TFM7 (E) and P119 (F). Each horizontal line represents the gene expression across the three developmental stages. For each gene, log2 expression ratios of DET1 variety versus T56 are normalized across the three stages. Red indicates upregulation and blue downregulation with respect to the T56 background. The z-scores have been used to indicate the deviation from normal distribution (the distribution standard derivation) and calculated from the variable's value minus the population's mean divided by the sd of the population. The vertical color bars next to gene trees indicate genes belonging to SOM classes in (C) and (D).

Article Snippet: Scanning of arrays was performed on a two-channel confocal microarray scanner (ScanArray5000; GSI Lumonics) with ScanArray software v3.1 (Packard Biochip Technologies).

Techniques: Transgenic Assay, Microarray, Expressing, Control, Gene Expression

Journal: The Plant Cell

Article Title: Integrative Transcript and Metabolite Analysis of Nutritionally Enhanced DE-ETIOLATED1 Downregulated Tomato Fruit ^[W]

doi: 10.1105/tpc.110.073866

Figure Lengend Snippet: The Effect of DET1 Downregulation on Photorespiration-Related Gene Expression Levels in P119 Mature Green Fruit. (A) Pathways and processes involved in photorespiration; steps in the pathways where transcripts have been measured are numbered. (B) Changes in gene expression levels relative to levels determined in control (T56 background) samples. Data from microarray analysis have been used; the experimental design of these experiments is provided in Methods. The data are expressed as means ± sd. Transcripts are labeled as follows, 1, ribulose-1,5-bisphosphate carboxylase small chain 3b; 2, glycolate oxidase; 3, hydroxypyruvate reductase; 4, glycine hydroxymethyl transferase; 5, transketolase; 6, phosphoglycolate phosphatase; 7, photosystem II protein 16; 8, photosystem II 22-kD protein; 9, photosystem II 5-kD protein; 10, photosystem II psbY; 11, photosystem II reaction center; 12, photosystem I subunit II; 13, photosystem I subunit III; 14, photosystem I subunit VI; 15, photosystem I subunit X; 16, photosystem I subunit psaN. Pa, pheophytin; Pq, plastoquinone; Cyt, cytochrome bf complex; Pc, plastocyanin; Fd, ferrodoxin; 3-PGA, 3-phosphoglycerate; GA-3-P, glyceraldehyde-3-phosphate. Stoichiometries of Calvin cycle components shown in parentheses.

Article Snippet: Scanning of arrays was performed on a two-channel confocal microarray scanner (ScanArray5000; GSI Lumonics) with ScanArray software v3.1 (Packard Biochip Technologies).

Techniques: Gene Expression, Control, Microarray, Labeling