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crispr guide rna design tool  (Benchling Inc)

 
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    Benchling Inc crispr guide rna design tool
    Crispr Guide Rna Design Tool, supplied by Benchling Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/tool/crispr+design+tool/pmc13155868-62-34-40
    Average 86 stars, based on 1 article reviews
    crispr guide rna design tool - by Bioz Stars, 2026-09
    86/100 stars

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    other:

    Article Title: RIN3 mutations impairing binding of the Alzheimer's disease-associated protein BIN1 lead to RAB5 hyperactivation and endosomal pathology.
    Article Snippet: The sgRNA sequences (table S1) were designed using an online tool (www.benchling.com/) and selected on the basis of their on- target score (104) and minimizing the predicted off- target effects.

    Article Title: RIN3 mutations impairing binding of the Alzheimer’s disease–associated protein BIN1 lead to RAB5 hyperactivation and endosomal pathology
    Article Snippet: The sgRNA sequences (table S1) were designed using an online tool ( www.benchling.com/ ) and selected on the basis of their on-target score ( ) and minimizing the predicted off-target effects.

    Article Title: An atypical F-type ATPase is necessary for the function of the antibody cleavage system MIB-MIP in mycoplasmas
    Article Snippet: The Cas9 nuclease target sequences were selected by using the “CRISPR Guides” tool available in the Benchling work environment ( https://benchling.com ).

    Clone Assay:

    Article Title: CXCR5 + monocyte emigration impairs the radiation-induced antitumor immune response.
    Article Snippet: RNA interference and sgRNA-mediated gene deletion Nonspecific control siRNA and siRNAs for HIF1α, Maf, and eIF4G2 were purchased from Sangon Biotech (China). siRNA transfection of cells was performed with Lipofectamine RNAiMAX Transfection Reagent following the manufacturer's instructions. .. Single-guide RNAs (sgRNAs) were designed using the Benching online tool (https://benchling.com/) and cloned into the lentiCRISPRv2 (52961). ..

    CRISPR:

    Article Title: FLInt 2.0: Robust and customizable single shot integration in C. elegans
    Article Snippet: .. crRNAs for CRISPR/Cas9 were designed using the “Design CRISPR Guides” tool on Benchling and evaluated for efficiency and specificity with the IDT CRISPR-Cas9 guide RNA checker. ..

    Article Title: Discovery and in vivo characterization of novel TOG domain-containing proteins using C. elegans
    Article Snippet: .. To identify the optimal PAM site we used ‘Design CRISPR’ tool in the electronic lab notebook Benchling. gRNAs and oligonucleotides are listed in Table S2. ..

    Article Title: An atypical F-type ATPase is necessary for the function of the antibody cleavage system MIB-MIP in mycoplasmas.
    Article Snippet: Plasmids for the expression of guide RNA in Saccharomyces cerevisiae. .. The Cas9 nuclease target sequences were selected by using the “CRISPR Guides” tool available in the Benchling work environment (https:// benchling.com). ..

    Sequencing:

    Article Title: Engineering Escherichia coli for high-level production of ergothioneine.
    Article Snippet: Ergothioneine (ERG) is a natural sulfur-containing compound derived from histidine that is known for its significant antioxidant properties.. Microbial biosynthesis of ERG has attracted considerable interest due to its sustainability and scalability.. Despite efforts to construct engineered strains, the ERG yield remains low.



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    RNA-seq profiling of human adipose-derived stem cells (hASCs) after 21 days of culture in myogenic <t>differentiation</t> <t>medium.</t> (a) Principal component analysis (PCA) based on transcriptome expression values (FPKM), showing clustering of biological replicates for Monolayer (2D), PCL, and Fibril conditions. (b) Venn diagram showing the overlap of detected genes among Monolayer, PCL, and Fibril groups (numbers indicate gene counts in each intersection). (c) Gene Ontology (GO) Biological Process (BP) over-representation analysis (ORA) for differentially expressed genes in 2D vs nFMBs (left) and PCL-mFiBs vs nFMBs (right); bars are plotted as −log10 (adjusted p value), with terms enriched among genes upregulated in the first condition shown to the right (red) and terms enriched among genes downregulated in nFMBs shown to the left (blue). (d) KEGG pathway enrichment analysis for differentially expressed genes between PCL-mFiBs and nFMBs groups; dot size represents the number of genes mapped to each pathway (Count), dot color indicates adjusted p value, and the x-axis denotes Gene Ratio. (e) Category network plot (CNP; category–gene network plot) for the PCL-mFiBs vs nFMBs comparison, visualizing representative enriched GO BP terms and their associated genes; gene nodes are colored by fold change and term nodes reflect enrichment significance. (f–i) Heatmaps of selected genes associated with representative GO terms: GO:0000280 (nuclear division), GO:0030198 (extracellular matrix organization), GO:0003012 <t>(muscle</t> system process), and GO:0007519 <t>(skeletal</t> muscle tissue development), respectively; expression patterns are shown across 2D, PCL-mFiBs, and nFMBs, with gene symbols listed alongside each heatmap.
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    RNA-seq profiling of human adipose-derived stem cells (hASCs) after 21 days of culture in myogenic <t>differentiation</t> <t>medium.</t> (a) Principal component analysis (PCA) based on transcriptome expression values (FPKM), showing clustering of biological replicates for Monolayer (2D), PCL, and Fibril conditions. (b) Venn diagram showing the overlap of detected genes among Monolayer, PCL, and Fibril groups (numbers indicate gene counts in each intersection). (c) Gene Ontology (GO) Biological Process (BP) over-representation analysis (ORA) for differentially expressed genes in 2D vs nFMBs (left) and PCL-mFiBs vs nFMBs (right); bars are plotted as −log10 (adjusted p value), with terms enriched among genes upregulated in the first condition shown to the right (red) and terms enriched among genes downregulated in nFMBs shown to the left (blue). (d) KEGG pathway enrichment analysis for differentially expressed genes between PCL-mFiBs and nFMBs groups; dot size represents the number of genes mapped to each pathway (Count), dot color indicates adjusted p value, and the x-axis denotes Gene Ratio. (e) Category network plot (CNP; category–gene network plot) for the PCL-mFiBs vs nFMBs comparison, visualizing representative enriched GO BP terms and their associated genes; gene nodes are colored by fold change and term nodes reflect enrichment significance. (f–i) Heatmaps of selected genes associated with representative GO terms: GO:0000280 (nuclear division), GO:0030198 (extracellular matrix organization), GO:0003012 <t>(muscle</t> system process), and GO:0007519 <t>(skeletal</t> muscle tissue development), respectively; expression patterns are shown across 2D, PCL-mFiBs, and nFMBs, with gene symbols listed alongside each heatmap.
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    Image Search Results


    RNA-seq profiling of human adipose-derived stem cells (hASCs) after 21 days of culture in myogenic differentiation medium. (a) Principal component analysis (PCA) based on transcriptome expression values (FPKM), showing clustering of biological replicates for Monolayer (2D), PCL, and Fibril conditions. (b) Venn diagram showing the overlap of detected genes among Monolayer, PCL, and Fibril groups (numbers indicate gene counts in each intersection). (c) Gene Ontology (GO) Biological Process (BP) over-representation analysis (ORA) for differentially expressed genes in 2D vs nFMBs (left) and PCL-mFiBs vs nFMBs (right); bars are plotted as −log10 (adjusted p value), with terms enriched among genes upregulated in the first condition shown to the right (red) and terms enriched among genes downregulated in nFMBs shown to the left (blue). (d) KEGG pathway enrichment analysis for differentially expressed genes between PCL-mFiBs and nFMBs groups; dot size represents the number of genes mapped to each pathway (Count), dot color indicates adjusted p value, and the x-axis denotes Gene Ratio. (e) Category network plot (CNP; category–gene network plot) for the PCL-mFiBs vs nFMBs comparison, visualizing representative enriched GO BP terms and their associated genes; gene nodes are colored by fold change and term nodes reflect enrichment significance. (f–i) Heatmaps of selected genes associated with representative GO terms: GO:0000280 (nuclear division), GO:0030198 (extracellular matrix organization), GO:0003012 (muscle system process), and GO:0007519 (skeletal muscle tissue development), respectively; expression patterns are shown across 2D, PCL-mFiBs, and nFMBs, with gene symbols listed alongside each heatmap.

    Journal: Bioactive Materials

    Article Title: Muscle-fiber-inspired nanofibrillar microbundles induce myogenic differentiation in human adipose-derived stem cells

    doi: 10.1016/j.bioactmat.2026.03.020

    Figure Lengend Snippet: RNA-seq profiling of human adipose-derived stem cells (hASCs) after 21 days of culture in myogenic differentiation medium. (a) Principal component analysis (PCA) based on transcriptome expression values (FPKM), showing clustering of biological replicates for Monolayer (2D), PCL, and Fibril conditions. (b) Venn diagram showing the overlap of detected genes among Monolayer, PCL, and Fibril groups (numbers indicate gene counts in each intersection). (c) Gene Ontology (GO) Biological Process (BP) over-representation analysis (ORA) for differentially expressed genes in 2D vs nFMBs (left) and PCL-mFiBs vs nFMBs (right); bars are plotted as −log10 (adjusted p value), with terms enriched among genes upregulated in the first condition shown to the right (red) and terms enriched among genes downregulated in nFMBs shown to the left (blue). (d) KEGG pathway enrichment analysis for differentially expressed genes between PCL-mFiBs and nFMBs groups; dot size represents the number of genes mapped to each pathway (Count), dot color indicates adjusted p value, and the x-axis denotes Gene Ratio. (e) Category network plot (CNP; category–gene network plot) for the PCL-mFiBs vs nFMBs comparison, visualizing representative enriched GO BP terms and their associated genes; gene nodes are colored by fold change and term nodes reflect enrichment significance. (f–i) Heatmaps of selected genes associated with representative GO terms: GO:0000280 (nuclear division), GO:0030198 (extracellular matrix organization), GO:0003012 (muscle system process), and GO:0007519 (skeletal muscle tissue development), respectively; expression patterns are shown across 2D, PCL-mFiBs, and nFMBs, with gene symbols listed alongside each heatmap.

    Article Snippet: For HSkMCs, myogenic differentiation was induced using Skeletal Muscle Differentiation Medium (ATCC, Manassas, USA).

    Techniques: RNA Sequencing, Derivative Assay, Cell Characterization, Expressing, Comparison