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Danaher Inc data analysis microarray slides
Percentage of probes that recognized four bacterial species tested by <t> microarray </t> analysis.

Data Analysis Microarray Slides, supplied by Danaher Inc, used in various techniques. Bioz Stars score: 94/100, based on 460 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/bladder+tissue+microarray+tma+slides/GenePix+Microarray+Systems/pmc06640225-367-2-14
Average 94 stars, based on 460 article reviews

data analysis microarray slides - by Bioz Stars, 2026-09

94/100 stars

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1) Product Images from "Distinguishing bacterial pathogens of potato using a genome‐wide microarray approach"

Article Title: Distinguishing bacterial pathogens of potato using a genome‐wide microarray approach

Journal: Molecular Plant Pathology

doi: 10.1111/j.1364-3703.2008.00482.x

Figure Legend Snippet: Percentage of probes that recognized four bacterial species tested by microarray analysis.

Techniques Used: Microarray

Scanned images of the signals detected on the microarray. A view of the whole microarray with eight subarrays is shown in (A), whereas areas covered by c. 800 probes (of the total of 9676 probes of one subarray) are shown at higher magnification in B and C. Total DNA extracted from pure cultures of bacteria and pooled from several strains of each species was used for hybridization. (A) Two samples were hybridized on each of the eight subarrays. The sample labelled with Cy5 (red) in all eight subarrays was Pectobacterium atrosepticum. The other samples labelled with Cy3 (illustrated as green) were (1) Streptomyces scabies, (2) Dickeya sp., (3) P. carotovorum, (4) Clavibacter michiganensis, (5) P. atrosepticum and (6–8) S. turgidiscabies. The amount of DNA per sample was 500 ng in subarrays 1–6. Signals were clear also with 50 ng of sample DNA (dilution 1 : 10, subarray 7). The image shown here was scanned using constant laser power and detector gain, and signals in subarray 8 (5 ng of DNA; dilution 1 : 100) cannot be seen. However, using increased detector gain, the most species‐specific signals (highest signal intensity) could be detected on subarray 8. (B) Magnification of a part of subarray 5: two samples of P. atrosepticum labelled each with a different dye. Intensive yellow spots (equal hybridization) correspond to probes specific to P. atrosepticum, whereas the spots with faint signal indicate non‐specific hybridization. (C) Magnification of part of the subarray 1: P. atrosepticum labelled with Cy5 and S. scabies labelled with Cy3. A ‘black spot’ (no signal) indicates no hybridization with the probe. The probes were designed to be gene‐specific, taking the whole‐genome sequence information of the species into consideration. Results indicate that most probes detect only the respective species based on which the probes were designed.

Figure Legend Snippet: Scanned images of the signals detected on the microarray. A view of the whole microarray with eight subarrays is shown in (A), whereas areas covered by c. 800 probes (of the total of 9676 probes of one subarray) are shown at higher magnification in B and C. Total DNA extracted from pure cultures of bacteria and pooled from several strains of each species was used for hybridization. (A) Two samples were hybridized on each of the eight subarrays. The sample labelled with Cy5 (red) in all eight subarrays was Pectobacterium atrosepticum. The other samples labelled with Cy3 (illustrated as green) were (1) Streptomyces scabies, (2) Dickeya sp., (3) P. carotovorum, (4) Clavibacter michiganensis, (5) P. atrosepticum and (6–8) S. turgidiscabies. The amount of DNA per sample was 500 ng in subarrays 1–6. Signals were clear also with 50 ng of sample DNA (dilution 1 : 10, subarray 7). The image shown here was scanned using constant laser power and detector gain, and signals in subarray 8 (5 ng of DNA; dilution 1 : 100) cannot be seen. However, using increased detector gain, the most species‐specific signals (highest signal intensity) could be detected on subarray 8. (B) Magnification of a part of subarray 5: two samples of P. atrosepticum labelled each with a different dye. Intensive yellow spots (equal hybridization) correspond to probes specific to P. atrosepticum, whereas the spots with faint signal indicate non‐specific hybridization. (C) Magnification of part of the subarray 1: P. atrosepticum labelled with Cy5 and S. scabies labelled with Cy3. A ‘black spot’ (no signal) indicates no hybridization with the probe. The probes were designed to be gene‐specific, taking the whole‐genome sequence information of the species into consideration. Results indicate that most probes detect only the respective species based on which the probes were designed.

Techniques Used: Microarray, Bacteria, Hybridization, Sequencing

Pooled DNA of the strains of Clavibacter michiganensis ssp. sepedonicus (Cms) (labelled with Cy3) and Pectobacterium atrosepticum (Pat) (labelled with Cy5) analysed on the microarray. (A) Scatterplot shows signal intensities from each probe on the array. Signals for Cms are given on the x‐axis and those for Pat on the y‐axis. Data reveal that the samples are not detected with common probes giving high signal intensities. (B) The scatterplot presented in a logarithmic domain places the probes within four groups: (1) high signal intensities for both samples (very few probes); (2) non‐specific probes detecting both samples (relatively low signal intensities); (3) probes giving high signal intensities only for Pat; and (4) probes giving high signal intensities only for Cms. In (C) (Cms) and (D) (Pat), the histograms of the logarithmic signal intensities show three peaks (histograms smoothened by the kernel density method). A threshold value of ~10 separates the two right‐most peaks (II and III) corresponding to the non‐specific and specific probes, respectively, as shown in B. The threshold value corresponds to the raw (non‐logarithmic) intensity value of c. 1000. In (E) (Cms) and (F) (Pat) the hybridization signal intensities are indicated per groups of probes. In the boxplot, the horizontal line in the middle of the box indicates the median value of the data. The box itself shows the first and third quartile of data. Whiskers outside the box indicate the range of data up to 1.5× the box height from both ends. Data beyond these limits are shown as circles. The intensity values of all probes are shown; however, in the final classification, the probes with intensities below the threshold obtained from the intensity histogram would be eliminated. Abbreviations used in the probe group names: Pat, P. atrosepticum; Sca, S. scabies; Cms, C. michiganensis spp. sepedonicus; IGS, 16S–23S intergenic spacer; Pca, P. carotovorum; IGS Dic, probes to the IGS of Dickeya spp.; Stu, S. turgidiscabies; Rso, R. solanacearum; nip, gene for necrosis‐inducing protein; Dic Nip30‐Nip50, probes of different lengths (30–50 nt) designed for the nip gene of D. dadantii; PAI, pathogenicity island.

Figure Legend Snippet: Pooled DNA of the strains of Clavibacter michiganensis ssp. sepedonicus (Cms) (labelled with Cy3) and Pectobacterium atrosepticum (Pat) (labelled with Cy5) analysed on the microarray. (A) Scatterplot shows signal intensities from each probe on the array. Signals for Cms are given on the x‐axis and those for Pat on the y‐axis. Data reveal that the samples are not detected with common probes giving high signal intensities. (B) The scatterplot presented in a logarithmic domain places the probes within four groups: (1) high signal intensities for both samples (very few probes); (2) non‐specific probes detecting both samples (relatively low signal intensities); (3) probes giving high signal intensities only for Pat; and (4) probes giving high signal intensities only for Cms. In (C) (Cms) and (D) (Pat), the histograms of the logarithmic signal intensities show three peaks (histograms smoothened by the kernel density method). A threshold value of ~10 separates the two right‐most peaks (II and III) corresponding to the non‐specific and specific probes, respectively, as shown in B. The threshold value corresponds to the raw (non‐logarithmic) intensity value of c. 1000. In (E) (Cms) and (F) (Pat) the hybridization signal intensities are indicated per groups of probes. In the boxplot, the horizontal line in the middle of the box indicates the median value of the data. The box itself shows the first and third quartile of data. Whiskers outside the box indicate the range of data up to 1.5× the box height from both ends. Data beyond these limits are shown as circles. The intensity values of all probes are shown; however, in the final classification, the probes with intensities below the threshold obtained from the intensity histogram would be eliminated. Abbreviations used in the probe group names: Pat, P. atrosepticum; Sca, S. scabies; Cms, C. michiganensis spp. sepedonicus; IGS, 16S–23S intergenic spacer; Pca, P. carotovorum; IGS Dic, probes to the IGS of Dickeya spp.; Stu, S. turgidiscabies; Rso, R. solanacearum; nip, gene for necrosis‐inducing protein; Dic Nip30‐Nip50, probes of different lengths (30–50 nt) designed for the nip gene of D. dadantii; PAI, pathogenicity island.

Techniques Used: Microarray, Hybridization

Pooled DNA of the strains of Streptomyces scabies (Sca) and S. turgidiscabies (Stu) analysed on the microarray. (A) Scatterplot showing signal intensities from each probe on the array. Signals for Sca are given on the x‐axis and those for Stu on the y‐axis. (B) The scatterplot presented on a logarithmic scale places the probes within four groups: (1) high signal intensities for both samples [of the total of 3894 probes designed to target genes of Sca, 1462 probes (c. 40%) show high signal intensities also for Stu]; (2) non‐specific probes giving relatively weak signals for both samples; (3) probes giving high signals only for Stu; and (4) probes giving high signals only for Sc. In (C) (Sca) and (D) (Stu), the histograms of the logarithmic signal intensities show three peaks corresponding to the groups of probes in B, as explained in Fig. 2. In (E) (Sca) and (F) (Stu) the hybridization signal intensities are indicated per three groups of probes. Interpretation of the boxplots is as in Fig. 1. The data indicate that the probes targeting the 16S–23S intergenic spacer (IGS) can be used to distinguish the two species.

Figure Legend Snippet: Pooled DNA of the strains of Streptomyces scabies (Sca) and S. turgidiscabies (Stu) analysed on the microarray. (A) Scatterplot showing signal intensities from each probe on the array. Signals for Sca are given on the x‐axis and those for Stu on the y‐axis. (B) The scatterplot presented on a logarithmic scale places the probes within four groups: (1) high signal intensities for both samples [of the total of 3894 probes designed to target genes of Sca, 1462 probes (c. 40%) show high signal intensities also for Stu]; (2) non‐specific probes giving relatively weak signals for both samples; (3) probes giving high signals only for Stu; and (4) probes giving high signals only for Sc. In (C) (Sca) and (D) (Stu), the histograms of the logarithmic signal intensities show three peaks corresponding to the groups of probes in B, as explained in Fig. 2. In (E) (Sca) and (F) (Stu) the hybridization signal intensities are indicated per three groups of probes. Interpretation of the boxplots is as in Fig. 1. The data indicate that the probes targeting the 16S–23S intergenic spacer (IGS) can be used to distinguish the two species.

Techniques Used: Microarray, Hybridization

Microarray:

Article Title: Unraveling the role of HDAC3 as an immunotherapy prognostic biomarker and therapeutic target in advanced non-small cell lung cancer
Article Snippet: The microarray was retrieved from − 80 °C storage and blocked with bovine serum albumin (BSA, 9048-46-8, Sigma) for 1.5 h. Following the blocking step, the microarray was incubated with plasma samples at a 1:1000 dilution for 1 h. After washing with 0.1% phosphate-buffered saline-Tween 20, the plates were incubated with Alexa Fluor 647 goat anti-human IgG (109-605-003, Jackson) diluted in 5% BSA. .. The microarray was then scanned using a GenePix 4300 A microarray scanner (141095, Molecular Devices) with a 635 nm excitation laser. .. Signal intensities of IgG for each protein were quantified using GenePix Pro v.6.0 software (Molecular Devices).

Article Title: Maackia amurensis seed lectin structure and sequence comparison with other M. amurensis lectins
Article Snippet: MASL, MAL2, and MAA lectins were biotinylated and hybridized (30 ug/ml) to Glycan Array 300 arrays (RayBiotech) which contain 300 triplicated synthetic glycans along with biotinylated protein positive controls and empty negative controls. .. Lectin binding was detected by incubation with Cy5 equivalent dye-conjugated streptavidin and visualized with a GenePix 4000B microarray laser scanner equipped with GenePix Pro version 7.2 software ( https://genepix-pro.software.informer.com/7.2 ) (Molecular Devices). .. Mean signal intensities were normalized to positive controls and analyzed using RayBio GA-Glycan-300-SW Analysis software ( https://www.raybiotech.com/glycan-array-300-ga-glycan-300 ) (RayBiotech).

Article Title: Biomarkers and immunogenic compositions for filarial parasites
Article Snippet: Chips were air dried by centrifugation at 500×g for 10 min, stored in a light proof desiccator for at least 2 hr and scanned on a GENEPIX® 4300 with Autoloader (Molecular Devices) using the 635 nm laser. .. Resulting 16-bit TIFF images were quantified using GENEPIX® Pro Microarray Analysis Software (Molecular Devices) and a GENEPIX® Array List (GAL) file. ..

Article Title: Supporting Information _ Lee and Fan _ Yale
Article Snippet: .. An Axon Genepix microarray scanner 4000B (Molecular Devices, USA) was used to image DRAQ5-stained cells (emitting 635 nm) on the STRQNW arrays. ..

other:

Article Title: Development of Lamprey-derived Antibodies Against Human Blood Group Antigens.
Article Snippet: A major challenge in the glycosciences is the scarcity of sensitive and specific glycanbinding reagents, such as monoclonal antibodies, for detecting and isolating glycans.. Here we report the development and characterization of new monoclonal antibodies (mAbs) that bind carbohydrate-based red blood cell (RBC) antigens including the ABO(H) antigens.. This approach exploits the immune system of the sea lamprey (Petromyzon marinus), which strongly responds to human glycans to enable the generation of high affinity antibodies.

Article Title: Development of lamprey-derived antibodies against human blood group antigens
Article Snippet: The scans were analyzed using GenePix (Molecular Devices) software and GLAD (GLycan Array Dashboard) software ( ).

Binding Assay:

Incubation:

Software:

Fluorescence:

Article Title: An African swine fever virus-specific antibody reactome reveals antigens as potential candidates for vaccine development
Article Snippet: After being washed three times and air-dried through brief centrifugation, the slides were scanned using a Genepix 4200A scanner (Molecular Devices, CA, USA). .. The median foreground and background fluorescence intensities were measured for each spot on the protein microarrays using GenePix Pro 6.0 (Molecular Devices, CA, USA). ..

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