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benchling sgrna design tool  (Benchling Inc)

 
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    Structured Review

    Benchling Inc benchling sgrna design tool
    Benchling Sgrna 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/sgrna+design+tool/crispr+design+tool/bio_rxiv__64898__2026__05__06__723379-256-7-7
    Average 86 stars, based on 1 article reviews
    benchling sgrna design tool - by Bioz Stars, 2026-10
    86/100 stars

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    Related Articles

    Sequencing:

    Article Title: Validation of reliable safe harbor locus for efficient porcine transgenesis.
    Article Snippet: Transgenic technology is now widely used in biomedical and agricultural fields.. Transgenesis is commonly achieved through random integration which might cause some uncertain consequences.. The site-specific integration could avoid this disadvantage.

    Cloning:

    Article Title: Loss-of-function variants affecting the STAGA complex component SUPT7L cause a developmental disorder with generalized lipodystrophy.
    Article Snippet: .. Cloning of CRISPR/Cas9 plasmid and generation of SUPT7L knockout HeLa cells The single guide RNA (sgRNA) targeting the third exon of human SUPT7L was designed using the Benchling sgRNA design tool (www.benchling.com) and was selected based on its predicted on- and off-target scores. .. The sgRNA was then cloned into the PX459 vector from Addgene (#62,988) as previously described (Ran et al. 2013).

    CRISPR:

    Article Title: Loss-of-function variants affecting the STAGA complex component SUPT7L cause a developmental disorder with generalized lipodystrophy.
    Article Snippet: .. Cloning of CRISPR/Cas9 plasmid and generation of SUPT7L knockout HeLa cells The single guide RNA (sgRNA) targeting the third exon of human SUPT7L was designed using the Benchling sgRNA design tool (www.benchling.com) and was selected based on its predicted on- and off-target scores. .. The sgRNA was then cloned into the PX459 vector from Addgene (#62,988) as previously described (Ran et al. 2013).

    Article Title: Super‐Enhancer Reprograming Driven by SOX9 and TCF7L2 Represents Transcription‐Targeted Therapeutic Vulnerability for Treating Gallbladder Cancer
    Article Snippet: For RNA interference (RNAi), two validated hairpins(sigma) were cloned into pLKO.1 (Addgene, #10878) by using AgeI and EcoRI site (Thermo Fisher Scientific), and a nontargeting shRNA was used as a negative control. .. For CRISPR interference (CRISPRi), sgRNA were designed using the online sgRNA design tool (https://www.benchling.com/), cloned into the lentiGuide-Puro (Addgene#52963) vector by using the BsmBI site (Thermo Fisher Scientific)1. .. Lenti-dCas9-KRAB-blast (Addgene, 89567) was used to express the dCas9-KRAB fusion protein.

    Plasmid Preparation:

    Article Title: Loss-of-function variants affecting the STAGA complex component SUPT7L cause a developmental disorder with generalized lipodystrophy.
    Article Snippet: .. Cloning of CRISPR/Cas9 plasmid and generation of SUPT7L knockout HeLa cells The single guide RNA (sgRNA) targeting the third exon of human SUPT7L was designed using the Benchling sgRNA design tool (www.benchling.com) and was selected based on its predicted on- and off-target scores. .. The sgRNA was then cloned into the PX459 vector from Addgene (#62,988) as previously described (Ran et al. 2013).

    Knock-Out:

    Article Title: Loss-of-function variants affecting the STAGA complex component SUPT7L cause a developmental disorder with generalized lipodystrophy.
    Article Snippet: .. Cloning of CRISPR/Cas9 plasmid and generation of SUPT7L knockout HeLa cells The single guide RNA (sgRNA) targeting the third exon of human SUPT7L was designed using the Benchling sgRNA design tool (www.benchling.com) and was selected based on its predicted on- and off-target scores. .. The sgRNA was then cloned into the PX459 vector from Addgene (#62,988) as previously described (Ran et al. 2013).



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    ( A ) A pie chart describing the different <t>sgRNA</t> sub-libraries. For each sub-library, the number of targeted genes and sgRNAs is specified (the number of genes is listed in brackets, and the number of sgRNAs is indicated within the pie chart). As non-targeting sgRNAs do not correspond to existing genes, the number of genes for this sub-library is not mentioned. ( B ) A volcano plot showing targeted gene hits from <t>tRNA-CRISPR</t> screen of HFF cell growth. The x-axis shows the Z-score of log2 fold change (FC) between competing cells (3 days of competition) and ancestor samples (median of log2 FC for all high-ranked sgRNAs per gene). The y-axis shows the –log10 FDR as calculated using the MAGeCK tool. The genes are marked according to the sub-libraries. Significance is determined by FDR < 0.05 and marked with dashed gray lines. All values are calculated for three biological repeats. ( C ) A heat map showing the (−log10) p -value of the hypergeometric test, which tests the enrichment of each sub-library in one of the following groups: significantly depleted in competing cells (log2FC < 0, FDR < 0.05) or significantly enriched in competing cells (log2FC > 0, FDR < 0.05). ( D ) Differences in the essentiality of tRNA isodecoders that are the sole targets of their corresponding sgRNA. tRNA essentiality is determined by the median log2 FC of its corresponding sgRNA between competing and ancestor cells. The arrow points towards higher tRNA essentiality. tRNA isoaceptors are denoted on the x-axis. Each dot corresponds to a different isodecoder type within the isoaceptor family. The number of isodecoders per tRNA family is mentioned in parentheses. ( E ) Comparison between the (log2) expression of the tRNA isodecoder in HFF (x-axis) and their essentiality, as shown in Fig. 5D (y-axis). The arrow points towards higher tRNA essentiality. Pearson correlation r = −0.41, p -value = 0.04.
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    ( A ) A pie chart describing the different <t>sgRNA</t> sub-libraries. For each sub-library, the number of targeted genes and sgRNAs is specified (the number of genes is listed in brackets, and the number of sgRNAs is indicated within the pie chart). As non-targeting sgRNAs do not correspond to existing genes, the number of genes for this sub-library is not mentioned. ( B ) A volcano plot showing targeted gene hits from <t>tRNA-CRISPR</t> screen of HFF cell growth. The x-axis shows the Z-score of log2 fold change (FC) between competing cells (3 days of competition) and ancestor samples (median of log2 FC for all high-ranked sgRNAs per gene). The y-axis shows the –log10 FDR as calculated using the MAGeCK tool. The genes are marked according to the sub-libraries. Significance is determined by FDR < 0.05 and marked with dashed gray lines. All values are calculated for three biological repeats. ( C ) A heat map showing the (−log10) p -value of the hypergeometric test, which tests the enrichment of each sub-library in one of the following groups: significantly depleted in competing cells (log2FC < 0, FDR < 0.05) or significantly enriched in competing cells (log2FC > 0, FDR < 0.05). ( D ) Differences in the essentiality of tRNA isodecoders that are the sole targets of their corresponding sgRNA. tRNA essentiality is determined by the median log2 FC of its corresponding sgRNA between competing and ancestor cells. The arrow points towards higher tRNA essentiality. tRNA isoaceptors are denoted on the x-axis. Each dot corresponds to a different isodecoder type within the isoaceptor family. The number of isodecoders per tRNA family is mentioned in parentheses. ( E ) Comparison between the (log2) expression of the tRNA isodecoder in HFF (x-axis) and their essentiality, as shown in Fig. 5D (y-axis). The arrow points towards higher tRNA essentiality. Pearson correlation r = −0.41, p -value = 0.04.
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    ( A ) A pie chart describing the different <t>sgRNA</t> sub-libraries. For each sub-library, the number of targeted genes and sgRNAs is specified (the number of genes is listed in brackets, and the number of sgRNAs is indicated within the pie chart). As non-targeting sgRNAs do not correspond to existing genes, the number of genes for this sub-library is not mentioned. ( B ) A volcano plot showing targeted gene hits from <t>tRNA-CRISPR</t> screen of HFF cell growth. The x-axis shows the Z-score of log2 fold change (FC) between competing cells (3 days of competition) and ancestor samples (median of log2 FC for all high-ranked sgRNAs per gene). The y-axis shows the –log10 FDR as calculated using the MAGeCK tool. The genes are marked according to the sub-libraries. Significance is determined by FDR < 0.05 and marked with dashed gray lines. All values are calculated for three biological repeats. ( C ) A heat map showing the (−log10) p -value of the hypergeometric test, which tests the enrichment of each sub-library in one of the following groups: significantly depleted in competing cells (log2FC < 0, FDR < 0.05) or significantly enriched in competing cells (log2FC > 0, FDR < 0.05). ( D ) Differences in the essentiality of tRNA isodecoders that are the sole targets of their corresponding sgRNA. tRNA essentiality is determined by the median log2 FC of its corresponding sgRNA between competing and ancestor cells. The arrow points towards higher tRNA essentiality. tRNA isoaceptors are denoted on the x-axis. Each dot corresponds to a different isodecoder type within the isoaceptor family. The number of isodecoders per tRNA family is mentioned in parentheses. ( E ) Comparison between the (log2) expression of the tRNA isodecoder in HFF (x-axis) and their essentiality, as shown in Fig. 5D (y-axis). The arrow points towards higher tRNA essentiality. Pearson correlation r = −0.41, p -value = 0.04.
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    ( A ) A pie chart describing the different <t>sgRNA</t> sub-libraries. For each sub-library, the number of targeted genes and sgRNAs is specified (the number of genes is listed in brackets, and the number of sgRNAs is indicated within the pie chart). As non-targeting sgRNAs do not correspond to existing genes, the number of genes for this sub-library is not mentioned. ( B ) A volcano plot showing targeted gene hits from <t>tRNA-CRISPR</t> screen of HFF cell growth. The x-axis shows the Z-score of log2 fold change (FC) between competing cells (3 days of competition) and ancestor samples (median of log2 FC for all high-ranked sgRNAs per gene). The y-axis shows the –log10 FDR as calculated using the MAGeCK tool. The genes are marked according to the sub-libraries. Significance is determined by FDR < 0.05 and marked with dashed gray lines. All values are calculated for three biological repeats. ( C ) A heat map showing the (−log10) p -value of the hypergeometric test, which tests the enrichment of each sub-library in one of the following groups: significantly depleted in competing cells (log2FC < 0, FDR < 0.05) or significantly enriched in competing cells (log2FC > 0, FDR < 0.05). ( D ) Differences in the essentiality of tRNA isodecoders that are the sole targets of their corresponding sgRNA. tRNA essentiality is determined by the median log2 FC of its corresponding sgRNA between competing and ancestor cells. The arrow points towards higher tRNA essentiality. tRNA isoaceptors are denoted on the x-axis. Each dot corresponds to a different isodecoder type within the isoaceptor family. The number of isodecoders per tRNA family is mentioned in parentheses. ( E ) Comparison between the (log2) expression of the tRNA isodecoder in HFF (x-axis) and their essentiality, as shown in Fig. 5D (y-axis). The arrow points towards higher tRNA essentiality. Pearson correlation r = −0.41, p -value = 0.04.
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    ( A ) A pie chart describing the different <t>sgRNA</t> sub-libraries. For each sub-library, the number of targeted genes and sgRNAs is specified (the number of genes is listed in brackets, and the number of sgRNAs is indicated within the pie chart). As non-targeting sgRNAs do not correspond to existing genes, the number of genes for this sub-library is not mentioned. ( B ) A volcano plot showing targeted gene hits from <t>tRNA-CRISPR</t> screen of HFF cell growth. The x-axis shows the Z-score of log2 fold change (FC) between competing cells (3 days of competition) and ancestor samples (median of log2 FC for all high-ranked sgRNAs per gene). The y-axis shows the –log10 FDR as calculated using the MAGeCK tool. The genes are marked according to the sub-libraries. Significance is determined by FDR < 0.05 and marked with dashed gray lines. All values are calculated for three biological repeats. ( C ) A heat map showing the (−log10) p -value of the hypergeometric test, which tests the enrichment of each sub-library in one of the following groups: significantly depleted in competing cells (log2FC < 0, FDR < 0.05) or significantly enriched in competing cells (log2FC > 0, FDR < 0.05). ( D ) Differences in the essentiality of tRNA isodecoders that are the sole targets of their corresponding sgRNA. tRNA essentiality is determined by the median log2 FC of its corresponding sgRNA between competing and ancestor cells. The arrow points towards higher tRNA essentiality. tRNA isoaceptors are denoted on the x-axis. Each dot corresponds to a different isodecoder type within the isoaceptor family. The number of isodecoders per tRNA family is mentioned in parentheses. ( E ) Comparison between the (log2) expression of the tRNA isodecoder in HFF (x-axis) and their essentiality, as shown in Fig. 5D (y-axis). The arrow points towards higher tRNA essentiality. Pearson correlation r = −0.41, p -value = 0.04.
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    benchling sgrna designer tool  (Benchling Inc)
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    ( A ) A pie chart describing the different <t>sgRNA</t> sub-libraries. For each sub-library, the number of targeted genes and sgRNAs is specified (the number of genes is listed in brackets, and the number of sgRNAs is indicated within the pie chart). As non-targeting sgRNAs do not correspond to existing genes, the number of genes for this sub-library is not mentioned. ( B ) A volcano plot showing targeted gene hits from <t>tRNA-CRISPR</t> screen of HFF cell growth. The x-axis shows the Z-score of log2 fold change (FC) between competing cells (3 days of competition) and ancestor samples (median of log2 FC for all high-ranked sgRNAs per gene). The y-axis shows the –log10 FDR as calculated using the MAGeCK tool. The genes are marked according to the sub-libraries. Significance is determined by FDR < 0.05 and marked with dashed gray lines. All values are calculated for three biological repeats. ( C ) A heat map showing the (−log10) p -value of the hypergeometric test, which tests the enrichment of each sub-library in one of the following groups: significantly depleted in competing cells (log2FC < 0, FDR < 0.05) or significantly enriched in competing cells (log2FC > 0, FDR < 0.05). ( D ) Differences in the essentiality of tRNA isodecoders that are the sole targets of their corresponding sgRNA. tRNA essentiality is determined by the median log2 FC of its corresponding sgRNA between competing and ancestor cells. The arrow points towards higher tRNA essentiality. tRNA isoaceptors are denoted on the x-axis. Each dot corresponds to a different isodecoder type within the isoaceptor family. The number of isodecoders per tRNA family is mentioned in parentheses. ( E ) Comparison between the (log2) expression of the tRNA isodecoder in HFF (x-axis) and their essentiality, as shown in Fig. 5D (y-axis). The arrow points towards higher tRNA essentiality. Pearson correlation r = −0.41, p -value = 0.04.
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    Image Search Results


    ( A ) A pie chart describing the different sgRNA sub-libraries. For each sub-library, the number of targeted genes and sgRNAs is specified (the number of genes is listed in brackets, and the number of sgRNAs is indicated within the pie chart). As non-targeting sgRNAs do not correspond to existing genes, the number of genes for this sub-library is not mentioned. ( B ) A volcano plot showing targeted gene hits from tRNA-CRISPR screen of HFF cell growth. The x-axis shows the Z-score of log2 fold change (FC) between competing cells (3 days of competition) and ancestor samples (median of log2 FC for all high-ranked sgRNAs per gene). The y-axis shows the –log10 FDR as calculated using the MAGeCK tool. The genes are marked according to the sub-libraries. Significance is determined by FDR < 0.05 and marked with dashed gray lines. All values are calculated for three biological repeats. ( C ) A heat map showing the (−log10) p -value of the hypergeometric test, which tests the enrichment of each sub-library in one of the following groups: significantly depleted in competing cells (log2FC < 0, FDR < 0.05) or significantly enriched in competing cells (log2FC > 0, FDR < 0.05). ( D ) Differences in the essentiality of tRNA isodecoders that are the sole targets of their corresponding sgRNA. tRNA essentiality is determined by the median log2 FC of its corresponding sgRNA between competing and ancestor cells. The arrow points towards higher tRNA essentiality. tRNA isoaceptors are denoted on the x-axis. Each dot corresponds to a different isodecoder type within the isoaceptor family. The number of isodecoders per tRNA family is mentioned in parentheses. ( E ) Comparison between the (log2) expression of the tRNA isodecoder in HFF (x-axis) and their essentiality, as shown in Fig. 5D (y-axis). The arrow points towards higher tRNA essentiality. Pearson correlation r = −0.41, p -value = 0.04.

    Journal: Molecular Systems Biology

    Article Title: Essentiality and dynamic expression of the human tRNA pool during viral infection

    doi: 10.1038/s44320-025-00181-7

    Figure Lengend Snippet: ( A ) A pie chart describing the different sgRNA sub-libraries. For each sub-library, the number of targeted genes and sgRNAs is specified (the number of genes is listed in brackets, and the number of sgRNAs is indicated within the pie chart). As non-targeting sgRNAs do not correspond to existing genes, the number of genes for this sub-library is not mentioned. ( B ) A volcano plot showing targeted gene hits from tRNA-CRISPR screen of HFF cell growth. The x-axis shows the Z-score of log2 fold change (FC) between competing cells (3 days of competition) and ancestor samples (median of log2 FC for all high-ranked sgRNAs per gene). The y-axis shows the –log10 FDR as calculated using the MAGeCK tool. The genes are marked according to the sub-libraries. Significance is determined by FDR < 0.05 and marked with dashed gray lines. All values are calculated for three biological repeats. ( C ) A heat map showing the (−log10) p -value of the hypergeometric test, which tests the enrichment of each sub-library in one of the following groups: significantly depleted in competing cells (log2FC < 0, FDR < 0.05) or significantly enriched in competing cells (log2FC > 0, FDR < 0.05). ( D ) Differences in the essentiality of tRNA isodecoders that are the sole targets of their corresponding sgRNA. tRNA essentiality is determined by the median log2 FC of its corresponding sgRNA between competing and ancestor cells. The arrow points towards higher tRNA essentiality. tRNA isoaceptors are denoted on the x-axis. Each dot corresponds to a different isodecoder type within the isoaceptor family. The number of isodecoders per tRNA family is mentioned in parentheses. ( E ) Comparison between the (log2) expression of the tRNA isodecoder in HFF (x-axis) and their essentiality, as shown in Fig. 5D (y-axis). The arrow points towards higher tRNA essentiality. Pearson correlation r = −0.41, p -value = 0.04.

    Article Snippet: CRISPR sgRNA design tool of Benchling , https://benchling.com , .

    Techniques: CRISPR, Comparison, Expressing

    ( A ) A schematic representation of the experimental setup and distributions of the measured GFP levels of uninfected HFF cells (upper panel), HCMV-infected HFF cells with non-targeting sgRNA (middle panel), and CRISPR-targeted and HCMV-infected HFF cells (lower panel). The percentage of cells in each of the GFP levels, GFP1-4, is marked in the middle and lower panels. ( B ) A volcano plot for targeted gene hits from tRNA-CRISPR screen in HCMV infection. The x-axis shows the Z-score of log2 FC between lowly infected cells (GFP2) and highly infected cells (GFP4). The y-axis shows the –log10 FDR as calculated from MAGeCK. The genes are marked according to the sub-libraries. Significance is determined by FDR < 0.05. All values are calculated for three biological repeats. ( C ) A heat map showing the (−log10) p -value of the hypergeometric test, which tests the enrichment of each sub-library in one of the following groups: significantly enriched in GFP2 cells (log2FC > 0, FDR < 0.05) or significantly depleted in GFP2 cells (log2FC < 0, FDR < 0.05). ( D ) The number of viral genomes estimated by the relative number of UL44 normalized to the B2M human gene, calculated by qPCR, in each individual CRISPR knockout. The dots in each bar depict three or four biological repeats. P -values represent statistical significance of differences between each group and the non-targeting control, as evaluated using Welch’s t-test with Holm correction for multiple comparisons. ( E , F ) Expression level (RPM) determined from tRNA-sequencing of ( E ) iMet-CAT-1-1 gene and ( F ) His-GTG-1-1 gene in cells targeted by non-targeting sgRNA (NT) or by sgRNAs corresponding to the tested tRNA. The dots in each bar depict three biological repeats. ( G ) A heat map describes the z-score log2FC between the different lowly infected cell populations (GFP1, GFP2, GFP3) and the highly infected cells (GFP4) for the significant gene hits. Genes found as significant hits in at least one of the comparisons are presented here. Non-significant hits are marked in gray squares. The genes are colored and marked according to their sub-library, corresponding to the colors and marker shapes described in the legend of Fig. 6B. The dendrogram depicts the similarity between the comparisons based on the enrichment gene hits pattern.

    Journal: Molecular Systems Biology

    Article Title: Essentiality and dynamic expression of the human tRNA pool during viral infection

    doi: 10.1038/s44320-025-00181-7

    Figure Lengend Snippet: ( A ) A schematic representation of the experimental setup and distributions of the measured GFP levels of uninfected HFF cells (upper panel), HCMV-infected HFF cells with non-targeting sgRNA (middle panel), and CRISPR-targeted and HCMV-infected HFF cells (lower panel). The percentage of cells in each of the GFP levels, GFP1-4, is marked in the middle and lower panels. ( B ) A volcano plot for targeted gene hits from tRNA-CRISPR screen in HCMV infection. The x-axis shows the Z-score of log2 FC between lowly infected cells (GFP2) and highly infected cells (GFP4). The y-axis shows the –log10 FDR as calculated from MAGeCK. The genes are marked according to the sub-libraries. Significance is determined by FDR < 0.05. All values are calculated for three biological repeats. ( C ) A heat map showing the (−log10) p -value of the hypergeometric test, which tests the enrichment of each sub-library in one of the following groups: significantly enriched in GFP2 cells (log2FC > 0, FDR < 0.05) or significantly depleted in GFP2 cells (log2FC < 0, FDR < 0.05). ( D ) The number of viral genomes estimated by the relative number of UL44 normalized to the B2M human gene, calculated by qPCR, in each individual CRISPR knockout. The dots in each bar depict three or four biological repeats. P -values represent statistical significance of differences between each group and the non-targeting control, as evaluated using Welch’s t-test with Holm correction for multiple comparisons. ( E , F ) Expression level (RPM) determined from tRNA-sequencing of ( E ) iMet-CAT-1-1 gene and ( F ) His-GTG-1-1 gene in cells targeted by non-targeting sgRNA (NT) or by sgRNAs corresponding to the tested tRNA. The dots in each bar depict three biological repeats. ( G ) A heat map describes the z-score log2FC between the different lowly infected cell populations (GFP1, GFP2, GFP3) and the highly infected cells (GFP4) for the significant gene hits. Genes found as significant hits in at least one of the comparisons are presented here. Non-significant hits are marked in gray squares. The genes are colored and marked according to their sub-library, corresponding to the colors and marker shapes described in the legend of Fig. 6B. The dendrogram depicts the similarity between the comparisons based on the enrichment gene hits pattern.

    Article Snippet: CRISPR sgRNA design tool of Benchling , https://benchling.com , .

    Techniques: Infection, CRISPR, Knock-Out, Control, Expressing, Sequencing, Marker