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customized whole-genome microarray  (NimbleGen Systems GmbH)

 
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    Structured Review

    NimbleGen Systems GmbH customized whole-genome microarray
    TABLE 4
    Customized Whole Genome Microarray, supplied by NimbleGen Systems GmbH, 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/custom+microarray/custom+microarrays/pmc04495223-84-2-22
    Average 90 stars, based on 1 article reviews
    customized whole-genome microarray - by Bioz Stars, 2026-10
    90/100 stars

    Images

    1) Product Images from "Survival of Listeria monocytogenes in Soil Requires AgrA-Mediated Regulation"

    Article Title: Survival of Listeria monocytogenes in Soil Requires AgrA-Mediated Regulation

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.04134-14

    TABLE 4
    Figure Legend Snippet: TABLE 4

    Techniques Used: Expressing, Mutagenesis, Microarray

    Related Articles

    other:

    Article Title: Vibrio cholerae CsrA Regulates ToxR Levels in Response to Amino Acids and Is Essential for Virulence
    Article Snippet: For microarray analysis, approximately 20 g RNA per sample was used to generate cDNA for hybridization to V. cholerae NimbleChip_X4 microarray slides (NimbleGen Systems, Roche Diagnostics Operations, Inc., Indianapolis, IN).

    Article Title: An insert in the covS gene distinguishes a pharyngeal and a blood isolate of Streptococcus pyogenes found in the same individual
    Article Snippet: Total RNA from early stationary phases between the two isolates were compared using custom Nimblegen Systems microarray chips.

    Article Title: Vibrio cholerae CsrA Regulates ToxR Levels in Response to Amino Acids and Is Essential for Virulence
    Article Snippet: For microarray analysis, approximately 20 μg RNA per sample was used to generate cDNA for hybridization to V. cholerae NimbleChip_X4 microarray slides (NimbleGen Systems, Roche Diagnostics Operations, Inc., Indianapolis, IN).

    Article Title: Listeria monocytogenes Differential Transcriptome Analysis Reveals Temperature-Dependent Agr Regulation and Suggests Overlaps with Other Regulons
    Article Snippet: A custom whole-genome microarray including all the 2857 annotated open reading frames (ORFs) of the genome of Listeria monocytogenes EGD-e was designed by NimbleGen Systems.

    Article Title: Survival of Listeria monocytogenes in Soil Requires AgrA-Mediated Regulation
    Article Snippet: A customized whole-genome microarray including the 2,857 annotated open reading frames (ORFs) of the genome of L. monocytogenes EGD-e was designed by NimbleGen Systems.

    Article Title: THE MOUSE RANKL GENE LOCUS IS DEFINED BY A BROAD PATTERN OF HISTONE ACETYLATION AND REGULATED THROUGH DISTINCT DISTAL ENHANCERS
    Article Snippet: These samples were then labeled according to the manufacturer’s ChIP-chip labeling recommendation (NimbleGen Systems, Madison, WI).

    Article Title: Identification and Characterization of a Novel Diterpene Gene Cluster in Aspergillus nidulans
    Article Snippet: The quality of RNA was assessed with the standard protocol of Agilent 2100 Bioanalyzer (Agilent Technologies).

    Microarray:

    Article Title: Succinic Semialdehyde Promotes Prosurvival Capability of Agrobacterium tumefaciens
    Article Snippet: The cDNA molecules were then fragmented into 50 to 200 nucleotides by partial digestion using DNase I (Promega) and labeled with biotin for microarray hybridization. .. The DNA microarray chips were synthesized by NimbleGen Systems (Madison, WI), and each chip included 4,661 open reading frames (ORFs) of the compiled genome sequence of A. tumefaciens strain C58 (University of Washington). ..

    Synthesized:

    Article Title: Succinic Semialdehyde Promotes Prosurvival Capability of Agrobacterium tumefaciens
    Article Snippet: The cDNA molecules were then fragmented into 50 to 200 nucleotides by partial digestion using DNase I (Promega) and labeled with biotin for microarray hybridization. .. The DNA microarray chips were synthesized by NimbleGen Systems (Madison, WI), and each chip included 4,661 open reading frames (ORFs) of the compiled genome sequence of A. tumefaciens strain C58 (University of Washington). ..

    Sequencing:

    Article Title: Succinic Semialdehyde Promotes Prosurvival Capability of Agrobacterium tumefaciens
    Article Snippet: The cDNA molecules were then fragmented into 50 to 200 nucleotides by partial digestion using DNase I (Promega) and labeled with biotin for microarray hybridization. .. The DNA microarray chips were synthesized by NimbleGen Systems (Madison, WI), and each chip included 4,661 open reading frames (ORFs) of the compiled genome sequence of A. tumefaciens strain C58 (University of Washington). ..



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    Image Search Results


    Mean microarray antigen spot intensities from TB-free badger serum samples at two time points following experimental infection. White bars represent TB-free sera; gray bars represent TB-infected sera collected at ( a ) 8 weeks and ( b ) 12–13 weeks post-infection. Mean microarray spot intensities (log 2 -normalized) are shown with 95% confidence interval error bars. Paired-sample t -tests were carried out comparing pre- and post-infection mean spot intensities. Antigens were ranked by BH-adjusted P -values, and the 10 most differential antigens (defined as those with the lowest BH-adjusted P -values) for each comparison group are shown. Significance levels: ns: P ≥ 0.05; *: P < 0.05; **: P < 0.01; and ***: P < 0.001.

    Journal: Journal of Clinical Microbiology

    Article Title: Proteome microarray-guided identification of mycobacterial antigens and ELISA-based peptide mapping for improved serological detection of Mycobacterium bovis infection in European badgers

    doi: 10.1128/jcm.01260-25

    Figure Lengend Snippet: Mean microarray antigen spot intensities from TB-free badger serum samples at two time points following experimental infection. White bars represent TB-free sera; gray bars represent TB-infected sera collected at ( a ) 8 weeks and ( b ) 12–13 weeks post-infection. Mean microarray spot intensities (log 2 -normalized) are shown with 95% confidence interval error bars. Paired-sample t -tests were carried out comparing pre- and post-infection mean spot intensities. Antigens were ranked by BH-adjusted P -values, and the 10 most differential antigens (defined as those with the lowest BH-adjusted P -values) for each comparison group are shown. Significance levels: ns: P ≥ 0.05; *: P < 0.05; **: P < 0.01; and ***: P < 0.001.

    Article Snippet: Translated proteins and IVTT controls were printed onto custom nitrocellulose-coated microarray slides (Grace Bio-Labs, Bend, OR, USA) using a GeneMachines OmniGrid Accent Microarray Printer.

    Techniques: Microarray, Infection, Comparison

    Mean microarray antigen spot intensities from TB-infected and BCG-vaccinated badger serum samples. Gray bars represent sera from TB-infected badgers collected 12–13 weeks after experimental infection; white bars represent sera from badgers that received ( a ) a single BCG vaccination or ( b ) two BCG vaccinations. Mean spot intensities (log₂-normalized) are shown with 95% confidence interval error bars. Independent-samples t -tests were used to compare antigen intensities between TB-infected and BCG-vaccinated groups. Antigens were ranked by BH-adjusted P -values, and the 10 most differential antigens (defined as those with the lowest BH-adjusted P -values) for each comparison group are shown; ***: P < 0.001.

    Journal: Journal of Clinical Microbiology

    Article Title: Proteome microarray-guided identification of mycobacterial antigens and ELISA-based peptide mapping for improved serological detection of Mycobacterium bovis infection in European badgers

    doi: 10.1128/jcm.01260-25

    Figure Lengend Snippet: Mean microarray antigen spot intensities from TB-infected and BCG-vaccinated badger serum samples. Gray bars represent sera from TB-infected badgers collected 12–13 weeks after experimental infection; white bars represent sera from badgers that received ( a ) a single BCG vaccination or ( b ) two BCG vaccinations. Mean spot intensities (log₂-normalized) are shown with 95% confidence interval error bars. Independent-samples t -tests were used to compare antigen intensities between TB-infected and BCG-vaccinated groups. Antigens were ranked by BH-adjusted P -values, and the 10 most differential antigens (defined as those with the lowest BH-adjusted P -values) for each comparison group are shown; ***: P < 0.001.

    Article Snippet: Translated proteins and IVTT controls were printed onto custom nitrocellulose-coated microarray slides (Grace Bio-Labs, Bend, OR, USA) using a GeneMachines OmniGrid Accent Microarray Printer.

    Techniques: Microarray, Infection, Comparison

    Dot-plot between anti-CRP antibodies and epitope positivity. The graph displays anti-CRP antibodies versus the number of positive epitopes obtained with microarray-based linear epitope mapping in patients with systemic lupus erythematosus ( n =42). (CRP, C-reactive protein).

    Journal: Frontiers in Immunology

    Article Title: Mapping autoantibody targets of full-length C-reactive protein in systemic lupus erythematosus: importance for neutrophil function and classical complement activation

    doi: 10.3389/fimmu.2025.1578372

    Figure Lengend Snippet: Dot-plot between anti-CRP antibodies and epitope positivity. The graph displays anti-CRP antibodies versus the number of positive epitopes obtained with microarray-based linear epitope mapping in patients with systemic lupus erythematosus ( n =42). (CRP, C-reactive protein).

    Article Snippet: The full sequence of the CRP monomer was printed in 15 a.a sequences with 14 a.a overlap using PEPperCHIP Custom Peptide Microarray (PEPperPRINT ® GmbH, Heidelberg, Germany).

    Techniques: Microarray

    Heatmap representation of autoreactivity against CRP obtained with microarray-based linear epitope mapping of the full CRP monomer. (A, B) Individual signal intensity of IgG autoantibody reactivity against full-length CRP for subjects with SLE ( n =42) and HBD ( n =11). (C–E) Mean signal intensity of IgG autoantibody reactivity against motifs of full-length CRP comparing anti-CRP negative (anti-CRP–; n =16) vs. anti-CRP positive (anti-CRP+; n =26) patients with SLE, patients with ( n =6) and without ( n =36) active disease, and no damage ( n =20) vs. irreversible organ damage (any organ system; n =22). Each column represents one subject (A, B) or the mean value of a group (C–E) . Each row represents a 15 amino acid long sequence covering the full length of the protein with 14 amino acids overlap and 7 amino acid GS repeats elongated before and after the protein sequence. (CRP, C-reactive protein; HBD, healthy blood donors; SDI, Systemic Lupus International Collaborating Clinics/American College of Rheumatology damage index; SLE, systemic lupus erythematosus; SLEDAI-2K, SLE Disease Activity Index 2000).

    Journal: Frontiers in Immunology

    Article Title: Mapping autoantibody targets of full-length C-reactive protein in systemic lupus erythematosus: importance for neutrophil function and classical complement activation

    doi: 10.3389/fimmu.2025.1578372

    Figure Lengend Snippet: Heatmap representation of autoreactivity against CRP obtained with microarray-based linear epitope mapping of the full CRP monomer. (A, B) Individual signal intensity of IgG autoantibody reactivity against full-length CRP for subjects with SLE ( n =42) and HBD ( n =11). (C–E) Mean signal intensity of IgG autoantibody reactivity against motifs of full-length CRP comparing anti-CRP negative (anti-CRP–; n =16) vs. anti-CRP positive (anti-CRP+; n =26) patients with SLE, patients with ( n =6) and without ( n =36) active disease, and no damage ( n =20) vs. irreversible organ damage (any organ system; n =22). Each column represents one subject (A, B) or the mean value of a group (C–E) . Each row represents a 15 amino acid long sequence covering the full length of the protein with 14 amino acids overlap and 7 amino acid GS repeats elongated before and after the protein sequence. (CRP, C-reactive protein; HBD, healthy blood donors; SDI, Systemic Lupus International Collaborating Clinics/American College of Rheumatology damage index; SLE, systemic lupus erythematosus; SLEDAI-2K, SLE Disease Activity Index 2000).

    Article Snippet: The full sequence of the CRP monomer was printed in 15 a.a sequences with 14 a.a overlap using PEPperCHIP Custom Peptide Microarray (PEPperPRINT ® GmbH, Heidelberg, Germany).

    Techniques: Microarray, Sequencing, Activity Assay