microarray laser scanner scanarray5000 Search Results


scanarray 5000 microarray scanner  (Lumonics Inc)
90
Lumonics Inc scanarray 5000 microarray scanner
Scanarray 5000 Microarray Scanner, supplied by Lumonics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/scanarray 5000 microarray scanner/product/Lumonics Inc
Average 90 stars, based on 1 article reviews
scanarray 5000 microarray scanner - by Bioz Stars, 2026-04
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two-channel confocal microarray scanner scanarray5000  (Lumonics Inc)
90
Lumonics Inc two-channel confocal microarray scanner scanarray5000
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 <t>microarray</t> 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).
Two Channel Confocal Microarray Scanner Scanarray5000, supplied by Lumonics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/two-channel confocal microarray scanner scanarray5000/product/Lumonics Inc
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two-channel confocal microarray scanner scanarray5000 - by Bioz Stars, 2026-04
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microarray laser scanner scanarray5000  (Packard Instruments)
90
Packard Instruments microarray laser scanner scanarray5000
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 <t>microarray</t> 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).
Microarray Laser Scanner Scanarray5000, supplied by Packard Instruments, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/microarray laser scanner scanarray5000/product/Packard Instruments
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microarray laser scanner scanarray5000 - by Bioz Stars, 2026-04
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scanarray 5000 confocal laser scanner  (GSI Lumonics Inc)
90
GSI Lumonics Inc scanarray 5000 confocal laser scanner
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 <t>microarray</t> 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).
Scanarray 5000 Confocal Laser Scanner, supplied by GSI Lumonics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/scanarray 5000 confocal laser scanner/product/GSI Lumonics Inc
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scanarray 5000 confocal laser scanner - by Bioz Stars, 2026-04
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streptavidin  (Lumonics Inc)
90
Lumonics Inc streptavidin
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 <t>microarray</t> 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).
Streptavidin, supplied by Lumonics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/streptavidin/product/Lumonics Inc
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streptavidin - by Bioz Stars, 2026-04
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first second antibodies (labelled cy3  (Lumonics Inc)
90
Lumonics Inc first second antibodies (labelled cy3
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 <t>microarray</t> 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).
First Second Antibodies (Labelled Cy3, supplied by Lumonics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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first second antibodies (labelled cy3 - by Bioz Stars, 2026-04
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iplab software  (Becton Dickinson)
90
Becton Dickinson iplab software
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 <t>microarray</t> 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).
Iplab Software, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/iplab software/product/Becton Dickinson
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iplab software - by Bioz Stars, 2026-04
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microarray suite 3.5 software  (scanalytics inc)
90
scanalytics inc microarray suite 3.5 software
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 <t>microarray</t> 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).
Microarray Suite 3.5 Software, supplied by scanalytics inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/microarray suite 3.5 software/product/scanalytics inc
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salmon testes dna  (Millipore)
90
Millipore salmon testes dna
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 <t>microarray</t> 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).
Salmon Testes Dna, supplied by Millipore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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iplab image processing software package  (scanalytics inc)
90
scanalytics inc iplab image processing software package
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 <t>microarray</t> 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).
Iplab Image Processing Software Package, supplied by scanalytics inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/iplab image processing software package/product/scanalytics inc
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disposable sterilization filtration units, 0.2-mm filter  (Thermo Fisher)
90
Thermo Fisher disposable sterilization filtration units, 0.2-mm filter
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 <t>microarray</t> 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).
Disposable Sterilization Filtration Units, 0.2 Mm Filter, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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sp5 confocal machine  (Danaher Inc)
86
Danaher Inc sp5 confocal machine
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 <t>microarray</t> 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).
Sp5 Confocal Machine, supplied by Danaher Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


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).

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

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.

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