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immunoinformatics  (Nikon)


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    Nikon immunoinformatics
    Immunoinformatics, supplied by Nikon, used in various techniques. Bioz Stars score: 99/100, based on 39798 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/immunoinformatics/NIS-Elements/pm39612244-220-231-235
    Average 99 stars, based on 39798 article reviews
    immunoinformatics - by Bioz Stars, 2026-09
    99/100 stars

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    Related Articles

    Recombinant:

    Article Title: Microglial APOE3 Christchurch protects neurons from Tau pathology in a human iPSC-based model of Alzheimer's disease.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER SAT1-R: 50- ACC AGG CTG AAA ATG TCT CTT CC -30 IDT, Coralville N/A TFRC-F: 50- ATC GGT TGG TGC CAC TGA ATG G -30 IDT, Coralville N/A TFRC-R: 50- ACA ACA GTG GGC TGG CAG AAA C -30 IDT, Coralville N/A ANXA3-F: 50- CTC CAC CAG CAG TCT TTG ATG C -30 IDT, Coralville N/A ANXA3-R: 50- CCT TCA TTT GCC TGC TTG TCC TG -30 IDT, Coralville N/A CD93-F: 50- GGC AGA CAG TTA CTC CTG GGT T -30 IDT, Coralville N/A CD93-R: 50- GGA GTT CAA AGC TCT GAG GAT GG-30 IDT, Coralville N/A SLC11A1-F: 50- CAT CCT CAC GTT CAC CAG CAT G -30 IDT, Coralville N/A SLC11A1-R: 50- CCA CGA AGT AGA GGT TGA TGG C-30 IDT, Coralville N/A ACSL1-F: 50- ATCAGGCTGCTCATGGATGACC-30 IDT, Coralville N/A ACSL1-R: 50- AGTCCAAGAGCCATCGCTTCAG-30 IDT, Coralville N/A ITGAX-F:50-GATGCTCAGAGATACTTCACGGC-30 IDT, Coralville N/A ITGAX-R: 50-CCACACCATCACTTCTGCGTTC-30 IDT, Coralville N/A GAPDH-F: 50- CCT GTT CGA CAG TCA GCC G-30 IDT, Coralville N/A GAPDH-R: 50-CGA CCA AAT CCG TTG ACT CC-30 IDT, Coralville N/A Recombinant DNA AAVS1-TRE3G-TFRC This study N/A pLVX-UbC-rtTA-Ngn2:2A:Ascl1 Addgene Cat # 127289 Software and algorithms ZEN software Carl Zeiss https://www.zeiss.com/microscopy/ us/products/microscope-software/zen.html Image-Pro Premier 9.1 Media Cybernetics http://www.mediacy.com/ support/imagepropremier AxIS software Axion Biosystems https://www.axionbiosystems.com/ products/axis-software AxIS Metrics Tool Axion Biosystems https://www.axionbiosystems.com/ products/axis-software NeuralMetric Tool Axion Biosystems https://www.axionbiosystems.com/ products/axis-software ClustVis N/A https://biit.cs.ut.ee/clustvis/ DAVID Bioinformatics Resources 6.8 Laboratory of Human Retrovirology and Immunoinformatics https://david.ncifcrf.gov/ NIS-Elements AR Nikon RRID: SCR_014329 Fiji Fiji RRID: SCR_002285 Graphpad Prism 10 Graphpad Software RRID: SCR_002798 Other CytoView MEA 12 plate Axion BioSystems Cat # M768-GL1-30Pt200-5 Maestro MEA system Axion BioSystems Equipment Hamamatsu EMCCD Hamamatsu Model C9100-13 Orbi-Shaker Benchmark Scientific NC0483060

    Software:

    Article Title: Microglial APOE3 Christchurch protects neurons from Tau pathology in a human iPSC-based model of Alzheimer's disease.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER SAT1-R: 50- ACC AGG CTG AAA ATG TCT CTT CC -30 IDT, Coralville N/A TFRC-F: 50- ATC GGT TGG TGC CAC TGA ATG G -30 IDT, Coralville N/A TFRC-R: 50- ACA ACA GTG GGC TGG CAG AAA C -30 IDT, Coralville N/A ANXA3-F: 50- CTC CAC CAG CAG TCT TTG ATG C -30 IDT, Coralville N/A ANXA3-R: 50- CCT TCA TTT GCC TGC TTG TCC TG -30 IDT, Coralville N/A CD93-F: 50- GGC AGA CAG TTA CTC CTG GGT T -30 IDT, Coralville N/A CD93-R: 50- GGA GTT CAA AGC TCT GAG GAT GG-30 IDT, Coralville N/A SLC11A1-F: 50- CAT CCT CAC GTT CAC CAG CAT G -30 IDT, Coralville N/A SLC11A1-R: 50- CCA CGA AGT AGA GGT TGA TGG C-30 IDT, Coralville N/A ACSL1-F: 50- ATCAGGCTGCTCATGGATGACC-30 IDT, Coralville N/A ACSL1-R: 50- AGTCCAAGAGCCATCGCTTCAG-30 IDT, Coralville N/A ITGAX-F:50-GATGCTCAGAGATACTTCACGGC-30 IDT, Coralville N/A ITGAX-R: 50-CCACACCATCACTTCTGCGTTC-30 IDT, Coralville N/A GAPDH-F: 50- CCT GTT CGA CAG TCA GCC G-30 IDT, Coralville N/A GAPDH-R: 50-CGA CCA AAT CCG TTG ACT CC-30 IDT, Coralville N/A Recombinant DNA AAVS1-TRE3G-TFRC This study N/A pLVX-UbC-rtTA-Ngn2:2A:Ascl1 Addgene Cat # 127289 Software and algorithms ZEN software Carl Zeiss https://www.zeiss.com/microscopy/ us/products/microscope-software/zen.html Image-Pro Premier 9.1 Media Cybernetics http://www.mediacy.com/ support/imagepropremier AxIS software Axion Biosystems https://www.axionbiosystems.com/ products/axis-software AxIS Metrics Tool Axion Biosystems https://www.axionbiosystems.com/ products/axis-software NeuralMetric Tool Axion Biosystems https://www.axionbiosystems.com/ products/axis-software ClustVis N/A https://biit.cs.ut.ee/clustvis/ DAVID Bioinformatics Resources 6.8 Laboratory of Human Retrovirology and Immunoinformatics https://david.ncifcrf.gov/ NIS-Elements AR Nikon RRID: SCR_014329 Fiji Fiji RRID: SCR_002285 Graphpad Prism 10 Graphpad Software RRID: SCR_002798 Other CytoView MEA 12 plate Axion BioSystems Cat # M768-GL1-30Pt200-5 Maestro MEA system Axion BioSystems Equipment Hamamatsu EMCCD Hamamatsu Model C9100-13 Orbi-Shaker Benchmark Scientific NC0483060

    Microelectrode Array:

    Article Title: Microglial APOE3 Christchurch protects neurons from Tau pathology in a human iPSC-based model of Alzheimer's disease.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER SAT1-R: 50- ACC AGG CTG AAA ATG TCT CTT CC -30 IDT, Coralville N/A TFRC-F: 50- ATC GGT TGG TGC CAC TGA ATG G -30 IDT, Coralville N/A TFRC-R: 50- ACA ACA GTG GGC TGG CAG AAA C -30 IDT, Coralville N/A ANXA3-F: 50- CTC CAC CAG CAG TCT TTG ATG C -30 IDT, Coralville N/A ANXA3-R: 50- CCT TCA TTT GCC TGC TTG TCC TG -30 IDT, Coralville N/A CD93-F: 50- GGC AGA CAG TTA CTC CTG GGT T -30 IDT, Coralville N/A CD93-R: 50- GGA GTT CAA AGC TCT GAG GAT GG-30 IDT, Coralville N/A SLC11A1-F: 50- CAT CCT CAC GTT CAC CAG CAT G -30 IDT, Coralville N/A SLC11A1-R: 50- CCA CGA AGT AGA GGT TGA TGG C-30 IDT, Coralville N/A ACSL1-F: 50- ATCAGGCTGCTCATGGATGACC-30 IDT, Coralville N/A ACSL1-R: 50- AGTCCAAGAGCCATCGCTTCAG-30 IDT, Coralville N/A ITGAX-F:50-GATGCTCAGAGATACTTCACGGC-30 IDT, Coralville N/A ITGAX-R: 50-CCACACCATCACTTCTGCGTTC-30 IDT, Coralville N/A GAPDH-F: 50- CCT GTT CGA CAG TCA GCC G-30 IDT, Coralville N/A GAPDH-R: 50-CGA CCA AAT CCG TTG ACT CC-30 IDT, Coralville N/A Recombinant DNA AAVS1-TRE3G-TFRC This study N/A pLVX-UbC-rtTA-Ngn2:2A:Ascl1 Addgene Cat # 127289 Software and algorithms ZEN software Carl Zeiss https://www.zeiss.com/microscopy/ us/products/microscope-software/zen.html Image-Pro Premier 9.1 Media Cybernetics http://www.mediacy.com/ support/imagepropremier AxIS software Axion Biosystems https://www.axionbiosystems.com/ products/axis-software AxIS Metrics Tool Axion Biosystems https://www.axionbiosystems.com/ products/axis-software NeuralMetric Tool Axion Biosystems https://www.axionbiosystems.com/ products/axis-software ClustVis N/A https://biit.cs.ut.ee/clustvis/ DAVID Bioinformatics Resources 6.8 Laboratory of Human Retrovirology and Immunoinformatics https://david.ncifcrf.gov/ NIS-Elements AR Nikon RRID: SCR_014329 Fiji Fiji RRID: SCR_002285 Graphpad Prism 10 Graphpad Software RRID: SCR_002798 Other CytoView MEA 12 plate Axion BioSystems Cat # M768-GL1-30Pt200-5 Maestro MEA system Axion BioSystems Equipment Hamamatsu EMCCD Hamamatsu Model C9100-13 Orbi-Shaker Benchmark Scientific NC0483060



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    Image Search Results


    Immunoinformatic strategy to identify MHC I and MHC II T cell epitopes. (A) The entire sequence of ZIKV strain PRVABC59 and 104 additional ZIKV strains were parsed into 9- and 10-mer frames, and conserved sequences predicted to bind to 6 MHC I supertypes and 9 common MHC II alleles were identified using Conservatrix and EpiMatrix algorithms. Promiscuous panDR clusters (DR) were generated from overlapping frames predicted to bind multiple MHC II alleles using the ClustiMer algorithm (16-27 amino acids). Sequences with high homology with human proteins (potential human cross-reactive sequences) were excluded using the JanusMatrix algorithm. (B) Shown is an example (Cluster DR1) of an EpiMatrix Cluster Report. Z-score indicates the potential of a 9-mer frame to bind to a given HLA allele; the strength of the score is indicated by the blue shading. Scores in the top 5% (Z-score ≥1.64) are considered “Hits”. *Z-scores in the top 10% are considered elevated, other scores grayed for simplicity. Frames containing four or more alleles scoring above 1.64 are referred to as EpiBars and are highlighted in yellow. Flanking amino acids, added to stabilize the cluster during in vitro testing, are underlined. The EpiMatrix Cluster Score is derived from the sum of Z-scores of EpiMatrix hits, normalized for the length of the cluster. Thus, EpiMatrix Cluster Score represents the excess or shortfall in predicted aggregate immunogenicity relative to a random peptide standard. Cluster Scores above 10 indicate significant potential for promiscuous response. (C) The 25-30 conserved ZIKV peptides predicted to bind the 6 MHC I supertypes and 33 clusters predicted to promiscuously bind human HLA-DR were synthesized for further study. The locations of each putative epitope or cluster within the ZIKV polyprotein are shown.

    Journal: Frontiers in Immunology

    Article Title: Identification of immunodominant T cell epitopes induced by natural Zika virus infection

    doi: 10.3389/fimmu.2023.1247876

    Figure Lengend Snippet: Immunoinformatic strategy to identify MHC I and MHC II T cell epitopes. (A) The entire sequence of ZIKV strain PRVABC59 and 104 additional ZIKV strains were parsed into 9- and 10-mer frames, and conserved sequences predicted to bind to 6 MHC I supertypes and 9 common MHC II alleles were identified using Conservatrix and EpiMatrix algorithms. Promiscuous panDR clusters (DR) were generated from overlapping frames predicted to bind multiple MHC II alleles using the ClustiMer algorithm (16-27 amino acids). Sequences with high homology with human proteins (potential human cross-reactive sequences) were excluded using the JanusMatrix algorithm. (B) Shown is an example (Cluster DR1) of an EpiMatrix Cluster Report. Z-score indicates the potential of a 9-mer frame to bind to a given HLA allele; the strength of the score is indicated by the blue shading. Scores in the top 5% (Z-score ≥1.64) are considered “Hits”. *Z-scores in the top 10% are considered elevated, other scores grayed for simplicity. Frames containing four or more alleles scoring above 1.64 are referred to as EpiBars and are highlighted in yellow. Flanking amino acids, added to stabilize the cluster during in vitro testing, are underlined. The EpiMatrix Cluster Score is derived from the sum of Z-scores of EpiMatrix hits, normalized for the length of the cluster. Thus, EpiMatrix Cluster Score represents the excess or shortfall in predicted aggregate immunogenicity relative to a random peptide standard. Cluster Scores above 10 indicate significant potential for promiscuous response. (C) The 25-30 conserved ZIKV peptides predicted to bind the 6 MHC I supertypes and 33 clusters predicted to promiscuously bind human HLA-DR were synthesized for further study. The locations of each putative epitope or cluster within the ZIKV polyprotein are shown.

    Article Snippet: Proprietary immunoinformatic tools developed at EpiVax were utilized for selection of putative T cell epitopes and epitope clusters.

    Techniques: Sequencing, Generated, In Vitro, Derivative Assay, Immunopeptidomics, Synthesized