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digitalgenome software  (MolecularWare Inc)

 
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    Structured Review

    MolecularWare Inc digitalgenome software
    Digitalgenome Software, supplied by MolecularWare 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/product/microarray+scanner+arrayworx+e/digitalgenome+software/pmc02752189-226-13-15
    Average 90 stars, based on 1 article reviews
    digitalgenome software - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    Labeling:

    Article Title: LPS hypersensitivity of gp130 mutant mice is independent of elevated haemopoietic TLR4 signaling.
    Article Snippet: Among the many inflammatory mediators induced by the prototypical inflammatory stimulus lipopolysaccharide (LPS), which signals via Toll-like receptor (TLR)-4, interleukin (IL)-6 has recently been shown to feedback and augment TLR4 signaling when overproduced in LPS hypersensitive gp130 F/F mice.. This regulation by IL-6 in gp130 F/F mice requires hyperactivation of the latent transcription factor signal transducer and activator of transcription (STAT) 3 via the IL-6 signaling receptor subunit gp130.. However, the identity of LPS/TLR4-responsive inflammatory signaling pathways and gene networks, which are modulated by IL-6 (via gp130/STAT3), and the extent to which the tissue and cellular context of this regulation contributes to LPS-induced endotoxic shock in gp130 F/F mice, are unknown.

    Amplification:

    Article Title: LPS hypersensitivity of gp130 mutant mice is independent of elevated haemopoietic TLR4 signaling.
    Article Snippet: Among the many inflammatory mediators induced by the prototypical inflammatory stimulus lipopolysaccharide (LPS), which signals via Toll-like receptor (TLR)-4, interleukin (IL)-6 has recently been shown to feedback and augment TLR4 signaling when overproduced in LPS hypersensitive gp130 F/F mice.. This regulation by IL-6 in gp130 F/F mice requires hyperactivation of the latent transcription factor signal transducer and activator of transcription (STAT) 3 via the IL-6 signaling receptor subunit gp130.. However, the identity of LPS/TLR4-responsive inflammatory signaling pathways and gene networks, which are modulated by IL-6 (via gp130/STAT3), and the extent to which the tissue and cellular context of this regulation contributes to LPS-induced endotoxic shock in gp130 F/F mice, are unknown.

    Microarray:

    Article Title: LPS hypersensitivity of gp130 mutant mice is independent of elevated haemopoietic TLR4 signaling.
    Article Snippet: Among the many inflammatory mediators induced by the prototypical inflammatory stimulus lipopolysaccharide (LPS), which signals via Toll-like receptor (TLR)-4, interleukin (IL)-6 has recently been shown to feedback and augment TLR4 signaling when overproduced in LPS hypersensitive gp130 F/F mice.. This regulation by IL-6 in gp130 F/F mice requires hyperactivation of the latent transcription factor signal transducer and activator of transcription (STAT) 3 via the IL-6 signaling receptor subunit gp130.. However, the identity of LPS/TLR4-responsive inflammatory signaling pathways and gene networks, which are modulated by IL-6 (via gp130/STAT3), and the extent to which the tissue and cellular context of this regulation contributes to LPS-induced endotoxic shock in gp130 F/F mice, are unknown.

    Software:

    Article Title: LPS hypersensitivity of gp130 mutant mice is independent of elevated haemopoietic TLR4 signaling.
    Article Snippet: Among the many inflammatory mediators induced by the prototypical inflammatory stimulus lipopolysaccharide (LPS), which signals via Toll-like receptor (TLR)-4, interleukin (IL)-6 has recently been shown to feedback and augment TLR4 signaling when overproduced in LPS hypersensitive gp130 F/F mice.. This regulation by IL-6 in gp130 F/F mice requires hyperactivation of the latent transcription factor signal transducer and activator of transcription (STAT) 3 via the IL-6 signaling receptor subunit gp130.. However, the identity of LPS/TLR4-responsive inflammatory signaling pathways and gene networks, which are modulated by IL-6 (via gp130/STAT3), and the extent to which the tissue and cellular context of this regulation contributes to LPS-induced endotoxic shock in gp130 F/F mice, are unknown.

    Article Title: Gene expression studies for the analysis of domoic acid production in the marine diatom Pseudo-nitzschia multiseries.
    Article Snippet: .. DigitalGenome software (MolecularWare, Cambridge, MA, USA) was then used to integrate annotated chip information with the tiff files and to visualize, edit and export the data for normalization. .. A loess algorithm was applied to the spot mean intensity values across replicate arrays within each biological experiment to correct for systematic biases using S+ArrayAnalyzer software (Insightful Corp., Seattle, WA, USA) [75,76].

    Article Title: The Antitumor Agent Imexon Activates Antioxidant Gene Expression: Evidence for an Oxidative Stress Response
    Article Snippet: After washing, slides were coated with DyeSaver2 (Genisphere, Inc., Hatfield, PA) according to the manufacturer’s instructions. .. Slides were scanned using a ScanArray Express 5000 (Perkin-Elmer Life Sciences, Boston, MA) and quantitation was done using the Digital Genome AnalyzerDG software package (MolecularWare, Inc., Cambridge, MA). ..

    Article Title: Gene expression studies for the analysis of domoic acid production in the marine diatom Pseudo-nitzschia multiseries
    Article Snippet: .. DigitalGenome software (MolecularWare, Cambridge, MA, USA) was then used to integrate annotated chip information with the tiff files and to visualize, edit and export the data for normalization. .. A loess algorithm was applied to the spot mean intensity values across replicate arrays within each biological experiment to correct for systematic biases using S+ArrayAnalyzer software (Insightful Corp., Seattle, WA, USA) [ , ].

    Article Title: Sparse Feature Selection Identifies H2A.Z as a Novel, Pattern-Specific Biomarker for Asymmetrically Self-Renewing Distributed Stem Cells
    Article Snippet: Hybridized microarrays were scanned with the arrayWoRx eTM Biochip Reader (Applied Precision LLC, Northwest Issaquah, WA). .. The fluorescence intensity of each spot was analyzed from the scanned tiff images by using the DigitalGenomeTM software (MolecularWare, Inc. Cambridge, MA). ..

    Quantitation Assay:

    Article Title: The Antitumor Agent Imexon Activates Antioxidant Gene Expression: Evidence for an Oxidative Stress Response
    Article Snippet: After washing, slides were coated with DyeSaver2 (Genisphere, Inc., Hatfield, PA) according to the manufacturer’s instructions. .. Slides were scanned using a ScanArray Express 5000 (Perkin-Elmer Life Sciences, Boston, MA) and quantitation was done using the Digital Genome AnalyzerDG software package (MolecularWare, Inc., Cambridge, MA). ..

    other:

    Article Title: Microarray analysis reveals difference in gene expression profiles of hair and wool sheep infected with Haemonchus contortus.
    Article Snippet: Sheep infected with the abomasal parasite, Haemonchus contortus, have reduced growth rates, decreased wool production, and anemia, and heavy infections may result in death.. Anthelmintic treatment can remove worms, but the cost of treatment and prevalence of drug-resistant worms has led to greater focus on genetic resistance of the host to parasitism.. Variation in parasite resistance exists within and among sheep breeds, and Caribbean hair sheep have greater resistance than most conventional wool breeds.

    Article Title: High throughput methods relating to microRNA expression analysis
    Article Snippet: A TIFF file of the scanned array is used for subsequent array analysis (DIGITAL GENOME SYSTEM SUITE, MOLECULARWARE, Cambridge, Mass.).

    Fluorescence:

    Article Title: Sparse Feature Selection Identifies H2A.Z as a Novel, Pattern-Specific Biomarker for Asymmetrically Self-Renewing Distributed Stem Cells
    Article Snippet: Hybridized microarrays were scanned with the arrayWoRx eTM Biochip Reader (Applied Precision LLC, Northwest Issaquah, WA). .. The fluorescence intensity of each spot was analyzed from the scanned tiff images by using the DigitalGenomeTM software (MolecularWare, Inc. Cambridge, MA). ..



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    Anabaena circinalis 131C putative specific sequences with protein matches in The National Center for Biotechnology Information (NCBI) protein database
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    Image Search Results


    a) microfluidic design: the device consists of two PDMS layers: flow (blue) and control (red). The chip is an array of eight rows by 48 columns for 384 unit cells. Each unit cell is composed of: two antibody chambers divided by a reaction chamber (1–2), 4 MITOMI buttons (3), a valve that segregates the unit cells (4), a valve that separates antibody and reaction chambers (5) and a valve for releasing pressure in the antibody chambers (6). b) The PDMS chip is aligned to an epoxy-functionalized slide onto which primary and secondary antibodies were spotted. c) Assay details: schematic of the unit cell and cross section of a button region: i) functionalization of the surface: BSA-biotin is flowed though the chip followed by neutravidin. Next, the buttons are closed and BSA-biotin flowed again to passivate all neutravidin molecules except for those located underneath the MITOMI buttons, ii) the biotinylated primary antibody is allowed to diffuse into the MITOMI detection chamber and is bound by neutravidin immobilizing it in the MITOMI detection regions, iii) the sample is flown through the device and antigens are captured by the surface immobilized antibodies, iv) finally, the fluorescently labeled secondary antibody is allowed to diffuse into the MITOMI area, binds to the antigen if present, and is trapped by MITOMI. The entire device is then quantitated using a DNA microarray scanner.

    Journal: PLoS ONE

    Article Title: A Microfluidic Platform for High-Throughput Multiplexed Protein Quantitation

    doi: 10.1371/journal.pone.0117744

    Figure Lengend Snippet: a) microfluidic design: the device consists of two PDMS layers: flow (blue) and control (red). The chip is an array of eight rows by 48 columns for 384 unit cells. Each unit cell is composed of: two antibody chambers divided by a reaction chamber (1–2), 4 MITOMI buttons (3), a valve that segregates the unit cells (4), a valve that separates antibody and reaction chambers (5) and a valve for releasing pressure in the antibody chambers (6). b) The PDMS chip is aligned to an epoxy-functionalized slide onto which primary and secondary antibodies were spotted. c) Assay details: schematic of the unit cell and cross section of a button region: i) functionalization of the surface: BSA-biotin is flowed though the chip followed by neutravidin. Next, the buttons are closed and BSA-biotin flowed again to passivate all neutravidin molecules except for those located underneath the MITOMI buttons, ii) the biotinylated primary antibody is allowed to diffuse into the MITOMI detection chamber and is bound by neutravidin immobilizing it in the MITOMI detection regions, iii) the sample is flown through the device and antigens are captured by the surface immobilized antibodies, iv) finally, the fluorescently labeled secondary antibody is allowed to diffuse into the MITOMI area, binds to the antigen if present, and is trapped by MITOMI. The entire device is then quantitated using a DNA microarray scanner.

    Article Snippet: The microfluidic device was scanned using a fluorescent microarray scanner (ArrayWorx e-Biochip Reader, Applied Precision, USA).

    Techniques: Control, Labeling, Microarray

    Anabaena circinalis 131C putative specific sequences with protein matches in The National Center for Biotechnology Information (NCBI) protein database

    Journal:

    Article Title: PCR-based positive hybridization to detect genomic diversity associated with bacterial secondary metabolism

    doi: 10.1093/nar/gnh012

    Figure Lengend Snippet: Anabaena circinalis 131C putative specific sequences with protein matches in The National Center for Biotechnology Information (NCBI) protein database

    Article Snippet: Microarray scanning, data acquisition and statistical analyses Clean slides were scanned with the ArrayWorx ‘e’ Microarray Scanner from Applied Precision, Inc. (Issaquah, WA).

    Techniques: Microarray, Hybridization

    Anabaena circinalis 344B putative specific sequences with protein matches (Id: identity; Sim: similarity) in the NCBI protein database

    Journal:

    Article Title: PCR-based positive hybridization to detect genomic diversity associated with bacterial secondary metabolism

    doi: 10.1093/nar/gnh012

    Figure Lengend Snippet: Anabaena circinalis 344B putative specific sequences with protein matches (Id: identity; Sim: similarity) in the NCBI protein database

    Article Snippet: Microarray scanning, data acquisition and statistical analyses Clean slides were scanned with the ArrayWorx ‘e’ Microarray Scanner from Applied Precision, Inc. (Issaquah, WA).

    Techniques: Microarray, Hybridization