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Benchling Inc benchling crispr design webtool

<t>CRISPR/Cas9-mediated</t> knockout of Mcu in RBL-2H3 cells. A , exon structure of rat Mcu indicating the target sites of guide RNA1 and guide RNA2. B , quantitative real-time PCR analysis of Mcu mRNA expression in wild-type (WT) RBL-2H3 cells and Mcu knockout (KO) clones A4 and D10 (n = 30 wells; 3 biological replicates). Medians ( bars ) with 95% confidence intervals (error bars ) are displayed on the scatter dot plots. C , immunoblot analysis of WT and Mcu KO clones A4 and D10 using MCU antibodies raised against either the C terminus or N terminus. Vinculin served as a loading control. Molecular weights are indicated in kilodaltons (kDa). MCU, mitochondrial Ca 2+ uniporter.

Benchling Crispr Design Webtool, 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/webtool/crispr+design+tool/pmc13197774-320-27-32
Average 86 stars, based on 1 article reviews

benchling crispr design webtool - by Bioz Stars, 2026-10

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1) Product Images from "Deletion of mitochondrial calcium uniporter enhances calcium signals by slowing calcium clearance and triggers adaptive transcriptomic remodeling"

Article Title: Deletion of mitochondrial calcium uniporter enhances calcium signals by slowing calcium clearance and triggers adaptive transcriptomic remodeling

Journal: The Journal of Biological Chemistry

doi: 10.1016/j.jbc.2026.111473

CRISPR/Cas9-mediated knockout of Mcu in RBL-2H3 cells. A , exon structure of rat Mcu indicating the target sites of guide RNA1 and guide RNA2. B , quantitative real-time PCR analysis of Mcu mRNA expression in wild-type (WT) RBL-2H3 cells and Mcu knockout (KO) clones A4 and D10 (n = 30 wells; 3 biological replicates). Medians ( bars ) with 95% confidence intervals (error bars ) are displayed on the scatter dot plots. C , immunoblot analysis of WT and Mcu KO clones A4 and D10 using MCU antibodies raised against either the C terminus or N terminus. Vinculin served as a loading control. Molecular weights are indicated in kilodaltons (kDa). MCU, mitochondrial Ca 2+ uniporter.

Figure Legend Snippet: CRISPR/Cas9-mediated knockout of Mcu in RBL-2H3 cells. A , exon structure of rat Mcu indicating the target sites of guide RNA1 and guide RNA2. B , quantitative real-time PCR analysis of Mcu mRNA expression in wild-type (WT) RBL-2H3 cells and Mcu knockout (KO) clones A4 and D10 (n = 30 wells; 3 biological replicates). Medians ( bars ) with 95% confidence intervals (error bars ) are displayed on the scatter dot plots. C , immunoblot analysis of WT and Mcu KO clones A4 and D10 using MCU antibodies raised against either the C terminus or N terminus. Vinculin served as a loading control. Molecular weights are indicated in kilodaltons (kDa). MCU, mitochondrial Ca 2+ uniporter.

Techniques Used: CRISPR, Knock-Out, Real-time Polymerase Chain Reaction, Expressing, Clone Assay, Western Blot, Control

Mcu knockout by CRISPR/Cas9 causes widespread and divergent transcriptomic changes across clones generated using distinct guide RNAs. A and B , volcano plots showing differentially expressed genes (DEGs) in Mcu −/− clones A4 ( A ) and D10 ( B ) relative to WT cells. Red and blue dots represent significantly upregulated and downregulated genes, respectively. Mcu is shown as a green dot . Gray dots indicate unchanged genes, either with below absolute fold change 2.0 cutoff ( light gray ) or having false discovery rate(FDR) higher than 0.05 ( dark gray ). C , volcano plot comparing A4 and D10 clones directly. D and E , Venn diagrams of downregulated genes ( D ) and upregulated genes ( E ) in A4 versus WT and D10 versus WT, highlighting both overlapping and clone-specific expression changes. F , ingenuity pathway analysis (IPA) of the 213 DEGs common to both clones (64 downregulated and 149 upregulated) with a z-score cutoff of 1.0. G , bubble plot displays enriched canonical pathways predicted by IPA. The y -axis on the right shows enriched pathway names ordered according to hierarchical clustering of their z-scores across two conditions (A4 versus WT and D10 versus WT), with the corresponding dendrogram displayed on the left . The x -axis labels the two conditions. Each pathway is represented by two circles , one for each condition. Circle size corresponds to the gene ratio for that pathway in the given condition. The fill color of each circle reflects the z-score: red for positive z-scores (activation), blue for negative z-scores (inhibition), transparent for values near zero, and gray where the z-score is NA. Threshold of z-score was set to absolute z-score ≥ 1.5. Below cutoff p values ( i.e. , p value > 0.05) are indicated by small lines on the right of the bubble. MCU, mitochondrial Ca 2+ uniporter.

Figure Legend Snippet: Mcu knockout by CRISPR/Cas9 causes widespread and divergent transcriptomic changes across clones generated using distinct guide RNAs. A and B , volcano plots showing differentially expressed genes (DEGs) in Mcu −/− clones A4 ( A ) and D10 ( B ) relative to WT cells. Red and blue dots represent significantly upregulated and downregulated genes, respectively. Mcu is shown as a green dot . Gray dots indicate unchanged genes, either with below absolute fold change 2.0 cutoff ( light gray ) or having false discovery rate(FDR) higher than 0.05 ( dark gray ). C , volcano plot comparing A4 and D10 clones directly. D and E , Venn diagrams of downregulated genes ( D ) and upregulated genes ( E ) in A4 versus WT and D10 versus WT, highlighting both overlapping and clone-specific expression changes. F , ingenuity pathway analysis (IPA) of the 213 DEGs common to both clones (64 downregulated and 149 upregulated) with a z-score cutoff of 1.0. G , bubble plot displays enriched canonical pathways predicted by IPA. The y -axis on the right shows enriched pathway names ordered according to hierarchical clustering of their z-scores across two conditions (A4 versus WT and D10 versus WT), with the corresponding dendrogram displayed on the left . The x -axis labels the two conditions. Each pathway is represented by two circles , one for each condition. Circle size corresponds to the gene ratio for that pathway in the given condition. The fill color of each circle reflects the z-score: red for positive z-scores (activation), blue for negative z-scores (inhibition), transparent for values near zero, and gray where the z-score is NA. Threshold of z-score was set to absolute z-score ≥ 1.5. Below cutoff p values ( i.e. , p value > 0.05) are indicated by small lines on the right of the bubble. MCU, mitochondrial Ca 2+ uniporter.

Techniques Used: Knock-Out, CRISPR, Clone Assay, Generated, Expressing, Activation Assay, Inhibition

Cloning:

Article Title: DRP1 and MID49 co-diffusion scans mitochondria for fission.
Article Snippet: .. For sgRNA design and cloning, sgRNAs targeting the human DRP1 locus (ENSG00000087470) near the start of the DRP1 open reading frame were designed using the CRISPR guide RNA design tools Benchling and CRISPOR. ..

CRISPR:

Article Title: Deletion of mitochondrial calcium uniporter enhances calcium signals by slowing calcium clearance and triggers adaptive transcriptomic remodeling
Article Snippet: .. Guide (g)RNA targeting human MCU (Ensembl Gene ID: ENSG00000156026 ; chromosomal location chr10 72,692,131—72,887,694 [+]; genome: GRCh38 (hg38, Homo sapiens )) was designed using the Benchling CRISPR design webtool. ..

Article Title: CYLD-mediated lysine63 deubiquitination regulates synaptic transmission and autophagy to mitigate age-related sequelae.
Article Snippet: .. A 200bp homology repair (HR) template flanking the mutation site introduced the desired edit TGT→TCT as well as two silent mutations creating a new XbaI site and destroying an existing EcoRI site to facilitate selection of mutagenized lines. crRNA and HR template were designed using the Benchling CRISPR design tool. tracrRNA, crRNA and HR template were ordered by IDT as RNAs and single stranded oligodeoxynucleotide (ssODN) respectively. ..

Article Title: Deletion of mitochondrial calcium uniporter enhances calcium signals by slowing calcium clearance and triggers adaptive transcriptomic remodeling
Article Snippet: .. Two different guide (g)RNAs targeting rat Mcu (Ensembl Gene ID: ENSRNOG00000045920 ; chromosomal location chr20 29,038,480—29,199,224 [-]; genome: Rnor_6.0 (rn6, Rattus norvegicus )) were designed using the Benchling CRISPR design webtool ( https://benchling.com/crispr ). ..

Mutagenesis:

Selection:

Injection:

Article Title: In vivo base editing alleviates hepatic iron accumulation and fibrosis in models of HFE-related hereditary hemochromatosis.
Article Snippet: .. Fig. 4: Off-target analysis and SNP/indel detection in RNA transcripts. (A) C282Y A>G correction rates in different organs of 129-Hfetm1.1Nca/J mice 4 months after injection of 2 mg/kg LNP-ABE-mG17 or PBS (n=4 LNP [n=8 hepatocytes], n=2 PBS [n=9 hepatocytes]), determined by NGS. (B) Nine top candidates of in silico–predicted off-target sites for Cas9/sgRNA mG17 (Benchling, CasOFF-Finder) with ≥2 mismatches or one bulge relative to the on-target sequence were selected for NGS analysis. (C) SNPs in exonic regions of mRNA transcripts, classified by functional consequence at 4 and 8 months after LNP-ABE-mG17 or PBS treatment. ..

Next-Generation Sequencing:

Sequencing:

Article Title: CRISPRi-assisted E. coli strains increase success rate of burdensome construct cloning
Article Snippet: .. Arbitrary sequences can be targeted using tools like Benchling for gRNA design; alternatively, known NGG PAMs can be used to determine the immediately preceding 20 bp of sequence on the same strand as the spacer sequence for the new gRNA. .. Then, the In-Fusion insert for the intermediate plasmid cloning can be ordered as complementary oligos from a DNA synthesis company like IDT with the following sequences flanking the new spacer: GATAATGGTTGCAGCTAGCxxxxxxxxxxxxxxxxxxxxGTTTTAGAGCTAGAAATAGC.

Functional Assay:

other:

Article Title: Ligustroflavone protects against acute kidney injury by inhibiting ferroptosis via acting on GSK3β/NRF2 signaling
Article Snippet: GSK3β-knockout (GSK3β-KO) TKPTs constructed: The CRISPR/Cas9 plasmids targeting mouse GSK3β [the guide (g) RNA sequences are presented in ] were constructed by using PX459 (cat. no. 62988; Addgene, Inc.).

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