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scanarray5000  (Packard Instruments)

 
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    Packard Instruments scanarray5000
    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/product/scanarray5000/scanarray+4000/pmc02722676-108-5-6
    Average 90 stars, based on 1 article reviews
    scanarray5000 - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    Extraction:

    Article Title: A Myc -regulated transcriptional network controls B-cell fate in response to BCR triggering
    Article Snippet: All samples were hybridized against amplified Universal Mouse Reference RNA (Stratagene, La Jolla, California, USA). .. Arrays were scanned with the ScanArray5000 (Packard Instruments, Rungis, France) or Genepix 4000B scanner, and feature extraction was performed with the Genepix Pro 4.0 software (Axon Instruments MDC, Sunnyvale, California, USA). .. Data analysis, including intensity-dependent Lowess normalization of the raw data, was done with GeneSpring 7.0 software (Agilent, Massy, France).

    Software:

    Article Title: A Myc -regulated transcriptional network controls B-cell fate in response to BCR triggering
    Article Snippet: All samples were hybridized against amplified Universal Mouse Reference RNA (Stratagene, La Jolla, California, USA). .. Arrays were scanned with the ScanArray5000 (Packard Instruments, Rungis, France) or Genepix 4000B scanner, and feature extraction was performed with the Genepix Pro 4.0 software (Axon Instruments MDC, Sunnyvale, California, USA). .. Data analysis, including intensity-dependent Lowess normalization of the raw data, was done with GeneSpring 7.0 software (Agilent, Massy, France).

    Article Title: Integration of Metabolism and Virulence by Clostridium difficile CodY
    Article Snippet: .. The microarray slides were scanned using a ScanArray 4000 (Packard Instrument Co.), and fluorescence intensities were quantified using ImaGene (BioDiscovery) software. .. Raw expression data from three arrays, representing three biological replicates, were normalized and averaged using GeneSpring (Agilent Technologies) software.

    Article Title: Normal Function of the Yeast TOR Pathway Requires the Type 2C Protein Phosphatase Ptc1
    Article Snippet: .. The scanner ScanArray 4000 (Packard Instrument Co.) was used to obtain the Cy3 and Cy5 images with a resolution of 10 m. The fluorescent intensity of the spots was measured and processed using GenePix Pro 6.0 software (Molecular Devices). ..

    Hybridization:

    Article Title: Loss of suppressor-of-fused function promotes tumorigenesis.
    Article Snippet: .. After hybridization and washing, fluorescence intensity was detected using ScanArray5000 (Packard Instruments, Meriden, CT, USA) and Genepix 4000B (Axon Instruments, Union City, CA, USA) scanners. (c) Representative Spectral Karyotyping (SKY) of chromosome 19 of Sufuþ / p53 / and Ptch1þ / medulloblastoma. ..

    Fluorescence:

    Article Title: Loss of suppressor-of-fused function promotes tumorigenesis.
    Article Snippet: .. After hybridization and washing, fluorescence intensity was detected using ScanArray5000 (Packard Instruments, Meriden, CT, USA) and Genepix 4000B (Axon Instruments, Union City, CA, USA) scanners. (c) Representative Spectral Karyotyping (SKY) of chromosome 19 of Sufuþ / p53 / and Ptch1þ / medulloblastoma. ..

    Article Title: Integration of Metabolism and Virulence by Clostridium difficile CodY
    Article Snippet: .. The microarray slides were scanned using a ScanArray 4000 (Packard Instrument Co.), and fluorescence intensities were quantified using ImaGene (BioDiscovery) software. .. Raw expression data from three arrays, representing three biological replicates, were normalized and averaged using GeneSpring (Agilent Technologies) software.

    Article Title: Genomic analysis of the Mozambique strain of Vibrio cholerae O1 reveals the origin of El Tor strains carrying classical CTX prophage
    Article Snippet: .. Hybridized, washed slides were scanned for Cy5 and Cy3 fluorescence intensities by using a ScanArray 5000 (Packard Instruments). .. The resulting files were analyzed by using GENEPIX 3.0 software (Axon Instruments, Foster City, CA).

    Microarray:

    Article Title: Integration of Metabolism and Virulence by Clostridium difficile CodY
    Article Snippet: .. The microarray slides were scanned using a ScanArray 4000 (Packard Instrument Co.), and fluorescence intensities were quantified using ImaGene (BioDiscovery) software. .. Raw expression data from three arrays, representing three biological replicates, were normalized and averaged using GeneSpring (Agilent Technologies) software.



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    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).
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    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).
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    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).
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    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).
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    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).
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    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).
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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