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genome scale crispri library  (Addgene inc)


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    Addgene inc genome scale crispri library
    ( A ) Experimental design of genome-scale perturb-seq in CD4+ T cells from multiple human donors across conditions (see Methods). ( B ) Number of cells (y-axis) for each biological sample (x-axis, condition-donor) with transcriptome passing quality control. Bars are colored by the outcome of guide RNA assignment (NTC: non-targeting controls). ( C ) Distribution of the number of cells harboring each gene perturbation (x-axis, log10 scale) across culture conditions (rows). The dotted line denotes the median. ( D ) Fraction of guides inducing significant on-target knock-down (y-axis) versus baseline expression of perturbed genes (x-axis). Each point represents 100 genes grouped by similar expression levels. Dotted vertical lines denote mean expression (log-normalized counts) per bin. ( E ) Comparison of trans effects between perturb-seq and arrayed knockout (KO) RNA-seq [ , ]: for each perturbed gene (x-axis), Pearson correlation of gene expression Log fold changes (LFCs) across all measured genes (y-axis) is shown. Blue bars: comparison of same gene perturbed in both platforms; grey bars: comparison on different perturbed genes. Error bars: 95% confidence interval (CI) from bootstrapping. Dotted line: theoretical maximum correlation given LFC noise. ( F ) Comparison of trans effects between perturb-seq and published <t>CRISPRi</t> FACS-based screens [ , , ]. For each measured gene (x-axis), Pearson correlation of expression LFCs across all perturbed genes (y-axis) is shown. Colored bars: same gene measured in both platforms; grey-scale bars: expression-matched different genes. Error bars: 95% CI from bootstrapping. Stimulation conditions of FACS screens are indicated below x-axis. ( G ) Pearson correlation between LFCs from downsampled and held-out validation data (5 lanes, all donors) for genes significant at 10% FDR. X-axis: fraction of perturbed cells (20–100%, ~55–450 cells). Colors: number of donors (1–4). Error bars: variability across independent downsampling splits and perturbed genes. Aggregated results across 12 perturbed genes are shown (see Suppl. Figure 9 for per-gene results). Grey dotted line: maximum correlation between perturbation effects in independent held-out splits.
    Genome Scale Crispri Library, supplied by Addgene inc, used in various techniques. Bioz Stars score: 94/100, based on 55 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/genome+scale+crispri+library/bio_rxiv__64898__2025__12__23__696273-493-1-8?v=Addgene+inc
    Average 94 stars, based on 55 article reviews
    genome scale crispri library - by Bioz Stars, 2026-07
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    1) Product Images from "Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits"

    Article Title: Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits

    Journal: bioRxiv

    doi: 10.64898/2025.12.23.696273

    ( A ) Experimental design of genome-scale perturb-seq in CD4+ T cells from multiple human donors across conditions (see Methods). ( B ) Number of cells (y-axis) for each biological sample (x-axis, condition-donor) with transcriptome passing quality control. Bars are colored by the outcome of guide RNA assignment (NTC: non-targeting controls). ( C ) Distribution of the number of cells harboring each gene perturbation (x-axis, log10 scale) across culture conditions (rows). The dotted line denotes the median. ( D ) Fraction of guides inducing significant on-target knock-down (y-axis) versus baseline expression of perturbed genes (x-axis). Each point represents 100 genes grouped by similar expression levels. Dotted vertical lines denote mean expression (log-normalized counts) per bin. ( E ) Comparison of trans effects between perturb-seq and arrayed knockout (KO) RNA-seq [ , ]: for each perturbed gene (x-axis), Pearson correlation of gene expression Log fold changes (LFCs) across all measured genes (y-axis) is shown. Blue bars: comparison of same gene perturbed in both platforms; grey bars: comparison on different perturbed genes. Error bars: 95% confidence interval (CI) from bootstrapping. Dotted line: theoretical maximum correlation given LFC noise. ( F ) Comparison of trans effects between perturb-seq and published CRISPRi FACS-based screens [ , , ]. For each measured gene (x-axis), Pearson correlation of expression LFCs across all perturbed genes (y-axis) is shown. Colored bars: same gene measured in both platforms; grey-scale bars: expression-matched different genes. Error bars: 95% CI from bootstrapping. Stimulation conditions of FACS screens are indicated below x-axis. ( G ) Pearson correlation between LFCs from downsampled and held-out validation data (5 lanes, all donors) for genes significant at 10% FDR. X-axis: fraction of perturbed cells (20–100%, ~55–450 cells). Colors: number of donors (1–4). Error bars: variability across independent downsampling splits and perturbed genes. Aggregated results across 12 perturbed genes are shown (see Suppl. Figure 9 for per-gene results). Grey dotted line: maximum correlation between perturbation effects in independent held-out splits.
    Figure Legend Snippet: ( A ) Experimental design of genome-scale perturb-seq in CD4+ T cells from multiple human donors across conditions (see Methods). ( B ) Number of cells (y-axis) for each biological sample (x-axis, condition-donor) with transcriptome passing quality control. Bars are colored by the outcome of guide RNA assignment (NTC: non-targeting controls). ( C ) Distribution of the number of cells harboring each gene perturbation (x-axis, log10 scale) across culture conditions (rows). The dotted line denotes the median. ( D ) Fraction of guides inducing significant on-target knock-down (y-axis) versus baseline expression of perturbed genes (x-axis). Each point represents 100 genes grouped by similar expression levels. Dotted vertical lines denote mean expression (log-normalized counts) per bin. ( E ) Comparison of trans effects between perturb-seq and arrayed knockout (KO) RNA-seq [ , ]: for each perturbed gene (x-axis), Pearson correlation of gene expression Log fold changes (LFCs) across all measured genes (y-axis) is shown. Blue bars: comparison of same gene perturbed in both platforms; grey bars: comparison on different perturbed genes. Error bars: 95% confidence interval (CI) from bootstrapping. Dotted line: theoretical maximum correlation given LFC noise. ( F ) Comparison of trans effects between perturb-seq and published CRISPRi FACS-based screens [ , , ]. For each measured gene (x-axis), Pearson correlation of expression LFCs across all perturbed genes (y-axis) is shown. Colored bars: same gene measured in both platforms; grey-scale bars: expression-matched different genes. Error bars: 95% CI from bootstrapping. Stimulation conditions of FACS screens are indicated below x-axis. ( G ) Pearson correlation between LFCs from downsampled and held-out validation data (5 lanes, all donors) for genes significant at 10% FDR. X-axis: fraction of perturbed cells (20–100%, ~55–450 cells). Colors: number of donors (1–4). Error bars: variability across independent downsampling splits and perturbed genes. Aggregated results across 12 perturbed genes are shown (see Suppl. Figure 9 for per-gene results). Grey dotted line: maximum correlation between perturbation effects in independent held-out splits.

    Techniques Used: Control, Knockdown, Expressing, Comparison, Knock-Out, RNA Sequencing, Gene Expression, Biomarker Discovery



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    ( A ) Experimental design of genome-scale perturb-seq in CD4+ T cells from multiple human donors across conditions (see Methods). ( B ) Number of cells (y-axis) for each biological sample (x-axis, condition-donor) with transcriptome passing quality control. Bars are colored by the outcome of guide RNA assignment (NTC: non-targeting controls). ( C ) Distribution of the number of cells harboring each gene perturbation (x-axis, log10 scale) across culture conditions (rows). The dotted line denotes the median. ( D ) Fraction of guides inducing significant on-target knock-down (y-axis) versus baseline expression of perturbed genes (x-axis). Each point represents 100 genes grouped by similar expression levels. Dotted vertical lines denote mean expression (log-normalized counts) per bin. ( E ) Comparison of trans effects between perturb-seq and arrayed knockout (KO) RNA-seq [ , ]: for each perturbed gene (x-axis), Pearson correlation of gene expression Log fold changes (LFCs) across all measured genes (y-axis) is shown. Blue bars: comparison of same gene perturbed in both platforms; grey bars: comparison on different perturbed genes. Error bars: 95% confidence interval (CI) from bootstrapping. Dotted line: theoretical maximum correlation given LFC noise. ( F ) Comparison of trans effects between perturb-seq and published <t>CRISPRi</t> FACS-based screens [ , , ]. For each measured gene (x-axis), Pearson correlation of expression LFCs across all perturbed genes (y-axis) is shown. Colored bars: same gene measured in both platforms; grey-scale bars: expression-matched different genes. Error bars: 95% CI from bootstrapping. Stimulation conditions of FACS screens are indicated below x-axis. ( G ) Pearson correlation between LFCs from downsampled and held-out validation data (5 lanes, all donors) for genes significant at 10% FDR. X-axis: fraction of perturbed cells (20–100%, ~55–450 cells). Colors: number of donors (1–4). Error bars: variability across independent downsampling splits and perturbed genes. Aggregated results across 12 perturbed genes are shown (see Suppl. Figure 9 for per-gene results). Grey dotted line: maximum correlation between perturbation effects in independent held-out splits.
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    ( A ) Experimental design of genome-scale perturb-seq in CD4+ T cells from multiple human donors across conditions (see Methods). ( B ) Number of cells (y-axis) for each biological sample (x-axis, condition-donor) with transcriptome passing quality control. Bars are colored by the outcome of guide RNA assignment (NTC: non-targeting controls). ( C ) Distribution of the number of cells harboring each gene perturbation (x-axis, log10 scale) across culture conditions (rows). The dotted line denotes the median. ( D ) Fraction of guides inducing significant on-target knock-down (y-axis) versus baseline expression of perturbed genes (x-axis). Each point represents 100 genes grouped by similar expression levels. Dotted vertical lines denote mean expression (log-normalized counts) per bin. ( E ) Comparison of trans effects between perturb-seq and arrayed knockout (KO) RNA-seq [ , ]: for each perturbed gene (x-axis), Pearson correlation of gene expression Log fold changes (LFCs) across all measured genes (y-axis) is shown. Blue bars: comparison of same gene perturbed in both platforms; grey bars: comparison on different perturbed genes. Error bars: 95% confidence interval (CI) from bootstrapping. Dotted line: theoretical maximum correlation given LFC noise. ( F ) Comparison of trans effects between perturb-seq and published <t>CRISPRi</t> FACS-based screens [ , , ]. For each measured gene (x-axis), Pearson correlation of expression LFCs across all perturbed genes (y-axis) is shown. Colored bars: same gene measured in both platforms; grey-scale bars: expression-matched different genes. Error bars: 95% CI from bootstrapping. Stimulation conditions of FACS screens are indicated below x-axis. ( G ) Pearson correlation between LFCs from downsampled and held-out validation data (5 lanes, all donors) for genes significant at 10% FDR. X-axis: fraction of perturbed cells (20–100%, ~55–450 cells). Colors: number of donors (1–4). Error bars: variability across independent downsampling splits and perturbed genes. Aggregated results across 12 perturbed genes are shown (see Suppl. Figure 9 for per-gene results). Grey dotted line: maximum correlation between perturbation effects in independent held-out splits.
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    ( A ) Experimental design of genome-scale perturb-seq in CD4+ T cells from multiple human donors across conditions (see Methods). ( B ) Number of cells (y-axis) for each biological sample (x-axis, condition-donor) with transcriptome passing quality control. Bars are colored by the outcome of guide RNA assignment (NTC: non-targeting controls). ( C ) Distribution of the number of cells harboring each gene perturbation (x-axis, log10 scale) across culture conditions (rows). The dotted line denotes the median. ( D ) Fraction of guides inducing significant on-target knock-down (y-axis) versus baseline expression of perturbed genes (x-axis). Each point represents 100 genes grouped by similar expression levels. Dotted vertical lines denote mean expression (log-normalized counts) per bin. ( E ) Comparison of trans effects between perturb-seq and arrayed knockout (KO) RNA-seq [ , ]: for each perturbed gene (x-axis), Pearson correlation of gene expression Log fold changes (LFCs) across all measured genes (y-axis) is shown. Blue bars: comparison of same gene perturbed in both platforms; grey bars: comparison on different perturbed genes. Error bars: 95% confidence interval (CI) from bootstrapping. Dotted line: theoretical maximum correlation given LFC noise. ( F ) Comparison of trans effects between perturb-seq and published CRISPRi FACS-based screens [ , , ]. For each measured gene (x-axis), Pearson correlation of expression LFCs across all perturbed genes (y-axis) is shown. Colored bars: same gene measured in both platforms; grey-scale bars: expression-matched different genes. Error bars: 95% CI from bootstrapping. Stimulation conditions of FACS screens are indicated below x-axis. ( G ) Pearson correlation between LFCs from downsampled and held-out validation data (5 lanes, all donors) for genes significant at 10% FDR. X-axis: fraction of perturbed cells (20–100%, ~55–450 cells). Colors: number of donors (1–4). Error bars: variability across independent downsampling splits and perturbed genes. Aggregated results across 12 perturbed genes are shown (see Suppl. Figure 9 for per-gene results). Grey dotted line: maximum correlation between perturbation effects in independent held-out splits.

    Journal: bioRxiv

    Article Title: Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits

    doi: 10.64898/2025.12.23.696273

    Figure Lengend Snippet: ( A ) Experimental design of genome-scale perturb-seq in CD4+ T cells from multiple human donors across conditions (see Methods). ( B ) Number of cells (y-axis) for each biological sample (x-axis, condition-donor) with transcriptome passing quality control. Bars are colored by the outcome of guide RNA assignment (NTC: non-targeting controls). ( C ) Distribution of the number of cells harboring each gene perturbation (x-axis, log10 scale) across culture conditions (rows). The dotted line denotes the median. ( D ) Fraction of guides inducing significant on-target knock-down (y-axis) versus baseline expression of perturbed genes (x-axis). Each point represents 100 genes grouped by similar expression levels. Dotted vertical lines denote mean expression (log-normalized counts) per bin. ( E ) Comparison of trans effects between perturb-seq and arrayed knockout (KO) RNA-seq [ , ]: for each perturbed gene (x-axis), Pearson correlation of gene expression Log fold changes (LFCs) across all measured genes (y-axis) is shown. Blue bars: comparison of same gene perturbed in both platforms; grey bars: comparison on different perturbed genes. Error bars: 95% confidence interval (CI) from bootstrapping. Dotted line: theoretical maximum correlation given LFC noise. ( F ) Comparison of trans effects between perturb-seq and published CRISPRi FACS-based screens [ , , ]. For each measured gene (x-axis), Pearson correlation of expression LFCs across all perturbed genes (y-axis) is shown. Colored bars: same gene measured in both platforms; grey-scale bars: expression-matched different genes. Error bars: 95% CI from bootstrapping. Stimulation conditions of FACS screens are indicated below x-axis. ( G ) Pearson correlation between LFCs from downsampled and held-out validation data (5 lanes, all donors) for genes significant at 10% FDR. X-axis: fraction of perturbed cells (20–100%, ~55–450 cells). Colors: number of donors (1–4). Error bars: variability across independent downsampling splits and perturbed genes. Aggregated results across 12 perturbed genes are shown (see Suppl. Figure 9 for per-gene results). Grey dotted line: maximum correlation between perturbation effects in independent held-out splits.

    Article Snippet: Our genome-scale CRISPRi library (to be available on Addgene) was cloned into PJY390 by Golden Gate Cloning as described previously [ ].

    Techniques: Control, Knockdown, Expressing, Comparison, Knock-Out, RNA Sequencing, Gene Expression, Biomarker Discovery