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bfp marked sgrna expression cassette  (Addgene inc)


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    Addgene inc bfp marked sgrna expression cassette
    A. Schematic illustrating how Human Accelerated Regions are defined. B. Upset graph showing the number of HAR targets represented in the Perturb-seq <t>sgRNA</t> library that intersect each of the annotations considered as evidence of neurodevelopmental or species-biased enhancer activity. C. Schematic of the direct-capture Perturb-seq experiment; see Methods for details. D. Schematic illustrating how sgRNAs were targeted to each HAR. Each was targeted by two high-scoring sgRNAs (Methods) within 300bp of the HAR. Targeted regions were located at least 2kb from any nearby promoter, if present. E. Expression of the NSC markers SOX2 and NES in hNSCs carrying KRAB:dCas9. F. The distribution of the number of high-quality cells in which an sgRNA could be assigned for each target. After filtering for cells bearing a single sgRNA, targets were represented by an average of ∼500 cells. G. Cumulative density plot showing the expression distribution of the indicated NSC marker genes in NTC-sgRNA bearing cells in the Perturb-seq screen. Expression values are normalized to the total number of UMI counts for each cell, multiplied by a scaling factor (1000), then log transformed. Schematics were generated in part using BioRender.com.
    Bfp Marked Sgrna Expression Cassette, supplied by Addgene inc, used in various techniques. Bioz Stars score: 88/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bfp marked sgrna expression cassette/product/Addgene inc
    Average 88 stars, based on 2 article reviews
    bfp marked sgrna expression cassette - by Bioz Stars, 2026-02
    88/100 stars

    Images

    1) Product Images from "Human Accelerated Regions regulate gene networks implicated in apical-to-basal neural progenitor fate transitions"

    Article Title: Human Accelerated Regions regulate gene networks implicated in apical-to-basal neural progenitor fate transitions

    Journal: bioRxiv

    doi: 10.1101/2024.06.30.601407

    A. Schematic illustrating how Human Accelerated Regions are defined. B. Upset graph showing the number of HAR targets represented in the Perturb-seq sgRNA library that intersect each of the annotations considered as evidence of neurodevelopmental or species-biased enhancer activity. C. Schematic of the direct-capture Perturb-seq experiment; see Methods for details. D. Schematic illustrating how sgRNAs were targeted to each HAR. Each was targeted by two high-scoring sgRNAs (Methods) within 300bp of the HAR. Targeted regions were located at least 2kb from any nearby promoter, if present. E. Expression of the NSC markers SOX2 and NES in hNSCs carrying KRAB:dCas9. F. The distribution of the number of high-quality cells in which an sgRNA could be assigned for each target. After filtering for cells bearing a single sgRNA, targets were represented by an average of ∼500 cells. G. Cumulative density plot showing the expression distribution of the indicated NSC marker genes in NTC-sgRNA bearing cells in the Perturb-seq screen. Expression values are normalized to the total number of UMI counts for each cell, multiplied by a scaling factor (1000), then log transformed. Schematics were generated in part using BioRender.com.
    Figure Legend Snippet: A. Schematic illustrating how Human Accelerated Regions are defined. B. Upset graph showing the number of HAR targets represented in the Perturb-seq sgRNA library that intersect each of the annotations considered as evidence of neurodevelopmental or species-biased enhancer activity. C. Schematic of the direct-capture Perturb-seq experiment; see Methods for details. D. Schematic illustrating how sgRNAs were targeted to each HAR. Each was targeted by two high-scoring sgRNAs (Methods) within 300bp of the HAR. Targeted regions were located at least 2kb from any nearby promoter, if present. E. Expression of the NSC markers SOX2 and NES in hNSCs carrying KRAB:dCas9. F. The distribution of the number of high-quality cells in which an sgRNA could be assigned for each target. After filtering for cells bearing a single sgRNA, targets were represented by an average of ∼500 cells. G. Cumulative density plot showing the expression distribution of the indicated NSC marker genes in NTC-sgRNA bearing cells in the Perturb-seq screen. Expression values are normalized to the total number of UMI counts for each cell, multiplied by a scaling factor (1000), then log transformed. Schematics were generated in part using BioRender.com.

    Techniques Used: Activity Assay, Expressing, Marker, Transformation Assay, Generated

    A. Effect sizes for HAR perturbations on gene module expression were estimated by multiple linear regression (MLR). The distribution of effect sizes in reference to NTC sgRNA-bearing cells, and associated FDRs, for each module’s expression from the MLR model are shown. Each point represents the overall effect of each HAR perturbation on that module. Points are colored by module membership as shown in . The horizontal line on each plot indicates an FDR significance threshold of 0.05. B . Donut plot showing the distribution of the number of significant effects (FDR < 0.05) for each HAR perturbation on module expression from the MLR model. C . A subset of HAR perturbations with significant effects. All perturbations with significant effects are shown in Figure S8. HARs are presented on the Y-axis. The upper panel shows HAR perturbations that significantly affect modules associated with polarity, while the lower panel shows perturbations that affect modules associated with other functions. Module expression effect sizes from the MLR model are plotted on the X-axis, and significance (-log10 FDR) is represented by point size. Module membership is represented by point color, and modules are categorized into general ontologies as in . Modules not showing significant effects (FDR < 0.05) are plotted in grey.
    Figure Legend Snippet: A. Effect sizes for HAR perturbations on gene module expression were estimated by multiple linear regression (MLR). The distribution of effect sizes in reference to NTC sgRNA-bearing cells, and associated FDRs, for each module’s expression from the MLR model are shown. Each point represents the overall effect of each HAR perturbation on that module. Points are colored by module membership as shown in . The horizontal line on each plot indicates an FDR significance threshold of 0.05. B . Donut plot showing the distribution of the number of significant effects (FDR < 0.05) for each HAR perturbation on module expression from the MLR model. C . A subset of HAR perturbations with significant effects. All perturbations with significant effects are shown in Figure S8. HARs are presented on the Y-axis. The upper panel shows HAR perturbations that significantly affect modules associated with polarity, while the lower panel shows perturbations that affect modules associated with other functions. Module expression effect sizes from the MLR model are plotted on the X-axis, and significance (-log10 FDR) is represented by point size. Module membership is represented by point color, and modules are categorized into general ontologies as in . Modules not showing significant effects (FDR < 0.05) are plotted in grey.

    Techniques Used: Expressing

    A. Representative images of day 7 NSCs transfected with a non-targeting sgRNA (NTC), an sgRNA targeting HAR181 (sgHAR181), and an sgRNA targeting CADM1 (sg CADM1 ), taken 4 days post-transfection. Localization of PARD3 is shown in green, NES is shown in red and DAPI nuclear staining is shown in blue. B. Quantification of the number of rosette-like cell groupings and unstructured cell groupings in each condition. Quantification was performed by 3 independent scorers blinded to the sgRNAs used. Mean counts for each type of cell grouping (rosette-like or unstructured) are shown as stacked bars. C. The ratio of rosette-like groupings to unstructured groupings in each condition. Significance was calculated via two-way ANOVA (with the sgRNA and replicate as variables), followed by Tukey post-hoc Honest Significant Difference tests across sgRNA treatments.
    Figure Legend Snippet: A. Representative images of day 7 NSCs transfected with a non-targeting sgRNA (NTC), an sgRNA targeting HAR181 (sgHAR181), and an sgRNA targeting CADM1 (sg CADM1 ), taken 4 days post-transfection. Localization of PARD3 is shown in green, NES is shown in red and DAPI nuclear staining is shown in blue. B. Quantification of the number of rosette-like cell groupings and unstructured cell groupings in each condition. Quantification was performed by 3 independent scorers blinded to the sgRNAs used. Mean counts for each type of cell grouping (rosette-like or unstructured) are shown as stacked bars. C. The ratio of rosette-like groupings to unstructured groupings in each condition. Significance was calculated via two-way ANOVA (with the sgRNA and replicate as variables), followed by Tukey post-hoc Honest Significant Difference tests across sgRNA treatments.

    Techniques Used: Transfection, Staining



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    A. Schematic illustrating how Human Accelerated Regions are defined. B. Upset graph showing the number of HAR targets represented in the Perturb-seq <t>sgRNA</t> library that intersect each of the annotations considered as evidence of neurodevelopmental or species-biased enhancer activity. C. Schematic of the direct-capture Perturb-seq experiment; see Methods for details. D. Schematic illustrating how sgRNAs were targeted to each HAR. Each was targeted by two high-scoring sgRNAs (Methods) within 300bp of the HAR. Targeted regions were located at least 2kb from any nearby promoter, if present. E. Expression of the NSC markers SOX2 and NES in hNSCs carrying KRAB:dCas9. F. The distribution of the number of high-quality cells in which an sgRNA could be assigned for each target. After filtering for cells bearing a single sgRNA, targets were represented by an average of ∼500 cells. G. Cumulative density plot showing the expression distribution of the indicated NSC marker genes in NTC-sgRNA bearing cells in the Perturb-seq screen. Expression values are normalized to the total number of UMI counts for each cell, multiplied by a scaling factor (1000), then log transformed. Schematics were generated in part using BioRender.com.
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    A. Schematic illustrating how Human Accelerated Regions are defined. B. Upset graph showing the number of HAR targets represented in the Perturb-seq <t>sgRNA</t> library that intersect each of the annotations considered as evidence of neurodevelopmental or species-biased enhancer activity. C. Schematic of the direct-capture Perturb-seq experiment; see Methods for details. D. Schematic illustrating how sgRNAs were targeted to each HAR. Each was targeted by two high-scoring sgRNAs (Methods) within 300bp of the HAR. Targeted regions were located at least 2kb from any nearby promoter, if present. E. Expression of the NSC markers SOX2 and NES in hNSCs carrying KRAB:dCas9. F. The distribution of the number of high-quality cells in which an sgRNA could be assigned for each target. After filtering for cells bearing a single sgRNA, targets were represented by an average of ∼500 cells. G. Cumulative density plot showing the expression distribution of the indicated NSC marker genes in NTC-sgRNA bearing cells in the Perturb-seq screen. Expression values are normalized to the total number of UMI counts for each cell, multiplied by a scaling factor (1000), then log transformed. Schematics were generated in part using BioRender.com.
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    Image Search Results


    A. Schematic illustrating how Human Accelerated Regions are defined. B. Upset graph showing the number of HAR targets represented in the Perturb-seq sgRNA library that intersect each of the annotations considered as evidence of neurodevelopmental or species-biased enhancer activity. C. Schematic of the direct-capture Perturb-seq experiment; see Methods for details. D. Schematic illustrating how sgRNAs were targeted to each HAR. Each was targeted by two high-scoring sgRNAs (Methods) within 300bp of the HAR. Targeted regions were located at least 2kb from any nearby promoter, if present. E. Expression of the NSC markers SOX2 and NES in hNSCs carrying KRAB:dCas9. F. The distribution of the number of high-quality cells in which an sgRNA could be assigned for each target. After filtering for cells bearing a single sgRNA, targets were represented by an average of ∼500 cells. G. Cumulative density plot showing the expression distribution of the indicated NSC marker genes in NTC-sgRNA bearing cells in the Perturb-seq screen. Expression values are normalized to the total number of UMI counts for each cell, multiplied by a scaling factor (1000), then log transformed. Schematics were generated in part using BioRender.com.

    Journal: bioRxiv

    Article Title: Human Accelerated Regions regulate gene networks implicated in apical-to-basal neural progenitor fate transitions

    doi: 10.1101/2024.06.30.601407

    Figure Lengend Snippet: A. Schematic illustrating how Human Accelerated Regions are defined. B. Upset graph showing the number of HAR targets represented in the Perturb-seq sgRNA library that intersect each of the annotations considered as evidence of neurodevelopmental or species-biased enhancer activity. C. Schematic of the direct-capture Perturb-seq experiment; see Methods for details. D. Schematic illustrating how sgRNAs were targeted to each HAR. Each was targeted by two high-scoring sgRNAs (Methods) within 300bp of the HAR. Targeted regions were located at least 2kb from any nearby promoter, if present. E. Expression of the NSC markers SOX2 and NES in hNSCs carrying KRAB:dCas9. F. The distribution of the number of high-quality cells in which an sgRNA could be assigned for each target. After filtering for cells bearing a single sgRNA, targets were represented by an average of ∼500 cells. G. Cumulative density plot showing the expression distribution of the indicated NSC marker genes in NTC-sgRNA bearing cells in the Perturb-seq screen. Expression values are normalized to the total number of UMI counts for each cell, multiplied by a scaling factor (1000), then log transformed. Schematics were generated in part using BioRender.com.

    Article Snippet: After 3 days of differentiation, cells were transfected via Amaxa Mouse NSC Nucleofection Kits (Lonza catalog #VPG-1004) with a BFP-marked sgRNA expression cassette (Addgene catalog #107722) containing an sgRNA targeting the GRN promoter, or containing a non-targeting control sgRNA.

    Techniques: Activity Assay, Expressing, Marker, Transformation Assay, Generated

    A. Effect sizes for HAR perturbations on gene module expression were estimated by multiple linear regression (MLR). The distribution of effect sizes in reference to NTC sgRNA-bearing cells, and associated FDRs, for each module’s expression from the MLR model are shown. Each point represents the overall effect of each HAR perturbation on that module. Points are colored by module membership as shown in . The horizontal line on each plot indicates an FDR significance threshold of 0.05. B . Donut plot showing the distribution of the number of significant effects (FDR < 0.05) for each HAR perturbation on module expression from the MLR model. C . A subset of HAR perturbations with significant effects. All perturbations with significant effects are shown in Figure S8. HARs are presented on the Y-axis. The upper panel shows HAR perturbations that significantly affect modules associated with polarity, while the lower panel shows perturbations that affect modules associated with other functions. Module expression effect sizes from the MLR model are plotted on the X-axis, and significance (-log10 FDR) is represented by point size. Module membership is represented by point color, and modules are categorized into general ontologies as in . Modules not showing significant effects (FDR < 0.05) are plotted in grey.

    Journal: bioRxiv

    Article Title: Human Accelerated Regions regulate gene networks implicated in apical-to-basal neural progenitor fate transitions

    doi: 10.1101/2024.06.30.601407

    Figure Lengend Snippet: A. Effect sizes for HAR perturbations on gene module expression were estimated by multiple linear regression (MLR). The distribution of effect sizes in reference to NTC sgRNA-bearing cells, and associated FDRs, for each module’s expression from the MLR model are shown. Each point represents the overall effect of each HAR perturbation on that module. Points are colored by module membership as shown in . The horizontal line on each plot indicates an FDR significance threshold of 0.05. B . Donut plot showing the distribution of the number of significant effects (FDR < 0.05) for each HAR perturbation on module expression from the MLR model. C . A subset of HAR perturbations with significant effects. All perturbations with significant effects are shown in Figure S8. HARs are presented on the Y-axis. The upper panel shows HAR perturbations that significantly affect modules associated with polarity, while the lower panel shows perturbations that affect modules associated with other functions. Module expression effect sizes from the MLR model are plotted on the X-axis, and significance (-log10 FDR) is represented by point size. Module membership is represented by point color, and modules are categorized into general ontologies as in . Modules not showing significant effects (FDR < 0.05) are plotted in grey.

    Article Snippet: After 3 days of differentiation, cells were transfected via Amaxa Mouse NSC Nucleofection Kits (Lonza catalog #VPG-1004) with a BFP-marked sgRNA expression cassette (Addgene catalog #107722) containing an sgRNA targeting the GRN promoter, or containing a non-targeting control sgRNA.

    Techniques: Expressing

    A. Representative images of day 7 NSCs transfected with a non-targeting sgRNA (NTC), an sgRNA targeting HAR181 (sgHAR181), and an sgRNA targeting CADM1 (sg CADM1 ), taken 4 days post-transfection. Localization of PARD3 is shown in green, NES is shown in red and DAPI nuclear staining is shown in blue. B. Quantification of the number of rosette-like cell groupings and unstructured cell groupings in each condition. Quantification was performed by 3 independent scorers blinded to the sgRNAs used. Mean counts for each type of cell grouping (rosette-like or unstructured) are shown as stacked bars. C. The ratio of rosette-like groupings to unstructured groupings in each condition. Significance was calculated via two-way ANOVA (with the sgRNA and replicate as variables), followed by Tukey post-hoc Honest Significant Difference tests across sgRNA treatments.

    Journal: bioRxiv

    Article Title: Human Accelerated Regions regulate gene networks implicated in apical-to-basal neural progenitor fate transitions

    doi: 10.1101/2024.06.30.601407

    Figure Lengend Snippet: A. Representative images of day 7 NSCs transfected with a non-targeting sgRNA (NTC), an sgRNA targeting HAR181 (sgHAR181), and an sgRNA targeting CADM1 (sg CADM1 ), taken 4 days post-transfection. Localization of PARD3 is shown in green, NES is shown in red and DAPI nuclear staining is shown in blue. B. Quantification of the number of rosette-like cell groupings and unstructured cell groupings in each condition. Quantification was performed by 3 independent scorers blinded to the sgRNAs used. Mean counts for each type of cell grouping (rosette-like or unstructured) are shown as stacked bars. C. The ratio of rosette-like groupings to unstructured groupings in each condition. Significance was calculated via two-way ANOVA (with the sgRNA and replicate as variables), followed by Tukey post-hoc Honest Significant Difference tests across sgRNA treatments.

    Article Snippet: After 3 days of differentiation, cells were transfected via Amaxa Mouse NSC Nucleofection Kits (Lonza catalog #VPG-1004) with a BFP-marked sgRNA expression cassette (Addgene catalog #107722) containing an sgRNA targeting the GRN promoter, or containing a non-targeting control sgRNA.

    Techniques: Transfection, Staining