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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/crispr+grna+design+tool/crispr+design+tool/pmc13155868-62-34-40
Average 86 stars, based on 1 article reviews
crispr guide rna design tool - by Bioz Stars, 2026-10
86/100 stars

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CRISPR:

Article Title: Streptococcus pyogenes EVs induce the alternative inflammasome via caspase-4/-5 in human monocytes
Article Snippet: .. Guide RNAs (gRNA) designed with CRISPR gRNA design tool (Benchling) or commercially predesigned were selected for high on-target and low off-target scores (Reagents and Tools Table). .. BLaER1 cells were transdifferentiated into monocyte-like cells for 7 days in six-well plates by seeding 10 6 cells/well in 3 mL of RPMI 1640 medium with Glutamax, 1% P/S, 10% FBS, 1% sodium pyruvate, 10 ng/mL of human recombinant IL-3, 10 ng/mL of human recombinant Macrophage Colony-stimulating Factor (both from PeproTech) and 100 nM of β-Estradiol (Sigma-Aldrich).

Article Title: Stereoselective methyl-swapping demonstrates target specificity of cognitive enhancer
Article Snippet: .. For CRISPR editing of the EIF2B4 gene in HEK293-Flp-In-T-rex cells, guide RNAs were designed using the Benchling CRISPR gRNA Design Tool, selecting the guide with the best on-target and off-target scores, and the L179V mutation within 10 bp of the cut site. ..

Article Title: Neural crest and periderm-specific requirements of Irf6 during neural tube and craniofacial development
Article Snippet: .. Guide RNAs (gRNA) were designed within the intronic regions flanking exons 3 and 4 using the CRISPR gRNA design tool from Benchling and were ordered from Synthego. ..

Article Title: Abnormal nucleoli architecture and aggregate formation in nucleophosmin mutated acute myeloid leukaemia
Article Snippet: .. DNA oligonucleotides (forward, 5′-ACATGGACATGAGCCCCCTG-3′; reverse 5′-GATAGTTCTGGGGCCTCAGG-3′) used for gRNA synthesis were designed using the Benchling CRISPR gRNA Design Tool available at https://www.benchling.com/ (accessed on 15 May 2022) and ordered through Sigma. .. gRNA was cloned into the Bbs1 restriction site of the pX330-U6-Chimeric_BB-CBh-hSpCAas9-hGem (1/110) vector ( Addgene #71707 ) before transformation into NEB 5-alpha Competent E. coli (New England Biolabs, Ipswich, MA, USA).

Article Title: Abnormal nucleoli architecture and aggregate formation in Nucleophosmin mutated Acute Myeloid Leukaemia.
Article Snippet: .. Generation of fluorescently tagged NPM1 HeLa cells using CRISPR/Cas9mediated gene editing DNA oligonucleotides (Forward 5’ ACATGGACATGAGCCCCCTG 3’, Reverse 5’ GATAGTTCTGGGGCCTCAGG 3’) used for gRNA synthesis were designed using the Benchling CRISPR gRNA Design Tool available at (www.benchling.com, accessed on 15 May 2022) and ordered through Sigma. gRNA was cloned into the Bbs1 restriction site of the pX330-U6-Chimeric_BB-CBh-hSpCAas9-hGem (1/110) vector (Addgene #71707) before transformation into NEB® 5-alpha Competent E. coli (New England Biolabs, Ipswich, Massachusetts, USA). .. DNA was prepared from single colonies before sequence verification using an Applied Biosystems™ (Waltham, Massachusetts, USA) 3130xl genetic analyser.

Article Title: Selective genome editing of amplified oncogenes triggers immunogenic cell death and tumor remodeling
Article Snippet: .. sgRNAs were designed using the Benchling CRISPR gRNA Design tool ( www.benchling.com ) and cloned into the LentiCRISPRv2 vector expressing Streptococcus pyogenes Cas9 (spCas9) (Addgene #52961). .. Cloning involved annealed and phosphorylated oligonucleotides (Sigma-Aldrich) targeting specific sequences, with transformations conducted in Stbl3 bacteria (Thermo Fisher Scientific).

Mutagenesis:

Article Title: Stereoselective methyl-swapping demonstrates target specificity of cognitive enhancer
Article Snippet: .. For CRISPR editing of the EIF2B4 gene in HEK293-Flp-In-T-rex cells, guide RNAs were designed using the Benchling CRISPR gRNA Design Tool, selecting the guide with the best on-target and off-target scores, and the L179V mutation within 10 bp of the cut site. ..

other:

Article Title: Massively parallel in vivo Perturb-seq screening.
Article Snippet: Advances in genomics have identified thousands of risk genes impacting human health and diseases, but the functions of these genes and their mechanistic contribution to disease are often unclear.. Moving beyond identification to actionable biological pathways requires dissecting risk gene function and cell type-specific action in intact tissues.. This gap can in part be addressed by in vivo Perturb-seq, a method that combines state-of-the-art gene editing tools for programmable perturbation of genes with highcontent, high-resolution single-cell genomic assays as phenotypic readouts.

Clone Assay:

Article Title: Abnormal nucleoli architecture and aggregate formation in Nucleophosmin mutated Acute Myeloid Leukaemia.
Article Snippet: .. Generation of fluorescently tagged NPM1 HeLa cells using CRISPR/Cas9mediated gene editing DNA oligonucleotides (Forward 5’ ACATGGACATGAGCCCCCTG 3’, Reverse 5’ GATAGTTCTGGGGCCTCAGG 3’) used for gRNA synthesis were designed using the Benchling CRISPR gRNA Design Tool available at (www.benchling.com, accessed on 15 May 2022) and ordered through Sigma. gRNA was cloned into the Bbs1 restriction site of the pX330-U6-Chimeric_BB-CBh-hSpCAas9-hGem (1/110) vector (Addgene #71707) before transformation into NEB® 5-alpha Competent E. coli (New England Biolabs, Ipswich, Massachusetts, USA). .. DNA was prepared from single colonies before sequence verification using an Applied Biosystems™ (Waltham, Massachusetts, USA) 3130xl genetic analyser.

Article Title: Selective genome editing of amplified oncogenes triggers immunogenic cell death and tumor remodeling
Article Snippet: .. sgRNAs were designed using the Benchling CRISPR gRNA Design tool ( www.benchling.com ) and cloned into the LentiCRISPRv2 vector expressing Streptococcus pyogenes Cas9 (spCas9) (Addgene #52961). .. Cloning involved annealed and phosphorylated oligonucleotides (Sigma-Aldrich) targeting specific sequences, with transformations conducted in Stbl3 bacteria (Thermo Fisher Scientific).

Transformation Assay:

Article Title: Abnormal nucleoli architecture and aggregate formation in Nucleophosmin mutated Acute Myeloid Leukaemia.
Article Snippet: .. Generation of fluorescently tagged NPM1 HeLa cells using CRISPR/Cas9mediated gene editing DNA oligonucleotides (Forward 5’ ACATGGACATGAGCCCCCTG 3’, Reverse 5’ GATAGTTCTGGGGCCTCAGG 3’) used for gRNA synthesis were designed using the Benchling CRISPR gRNA Design Tool available at (www.benchling.com, accessed on 15 May 2022) and ordered through Sigma. gRNA was cloned into the Bbs1 restriction site of the pX330-U6-Chimeric_BB-CBh-hSpCAas9-hGem (1/110) vector (Addgene #71707) before transformation into NEB® 5-alpha Competent E. coli (New England Biolabs, Ipswich, Massachusetts, USA). .. DNA was prepared from single colonies before sequence verification using an Applied Biosystems™ (Waltham, Massachusetts, USA) 3130xl genetic analyser.

Plasmid Preparation:

Article Title: Selective genome editing of amplified oncogenes triggers immunogenic cell death and tumor remodeling
Article Snippet: .. sgRNAs were designed using the Benchling CRISPR gRNA Design tool ( www.benchling.com ) and cloned into the LentiCRISPRv2 vector expressing Streptococcus pyogenes Cas9 (spCas9) (Addgene #52961). .. Cloning involved annealed and phosphorylated oligonucleotides (Sigma-Aldrich) targeting specific sequences, with transformations conducted in Stbl3 bacteria (Thermo Fisher Scientific).

Article Title: Selective genome editing of amplified oncogenes triggers immunogenic cell death and tumor remodeling.
Article Snippet: Dose-dependent treatments with DOX (S1208, Selleckchem) were applied: 0.02 μM for IMR-32A, 0.1 μM for LAN-5A, 0.3 μM for KELLYA, 0.5 μM for SK-N-FINA and 1.75 μM for SK-N-ASNA. tdTomato+ IMR-32A cells were generated via transduction with LVs using the pUltra-Chili-Luc transfer plasmid (Addgene #48688), followed by cell sorting. .. All cell lines were regularly tested to absence of mycoplasma contamination. sgRNA design and vector construction. sgRNAs were designed using the Benchling CRISPR gRNA Design tool (www.benchling.com) and cloned into the LentiCRISPRv2 vector expressing Streptococcus pyogenes Cas9 (spCas9) (Addgene #52961). .. Cloning involved annealed and phosphorylated oligonucleotides (Sigma-Aldrich) targeting specific sequences, with transformations conducted in Stbl3 bacteria (Thermo Fisher Scientific).

Expressing:

Article Title: Selective genome editing of amplified oncogenes triggers immunogenic cell death and tumor remodeling
Article Snippet: .. sgRNAs were designed using the Benchling CRISPR gRNA Design tool ( www.benchling.com ) and cloned into the LentiCRISPRv2 vector expressing Streptococcus pyogenes Cas9 (spCas9) (Addgene #52961). .. Cloning involved annealed and phosphorylated oligonucleotides (Sigma-Aldrich) targeting specific sequences, with transformations conducted in Stbl3 bacteria (Thermo Fisher Scientific).

Article Title: Selective genome editing of amplified oncogenes triggers immunogenic cell death and tumor remodeling.
Article Snippet: Dose-dependent treatments with DOX (S1208, Selleckchem) were applied: 0.02 μM for IMR-32A, 0.1 μM for LAN-5A, 0.3 μM for KELLYA, 0.5 μM for SK-N-FINA and 1.75 μM for SK-N-ASNA. tdTomato+ IMR-32A cells were generated via transduction with LVs using the pUltra-Chili-Luc transfer plasmid (Addgene #48688), followed by cell sorting. .. All cell lines were regularly tested to absence of mycoplasma contamination. sgRNA design and vector construction. sgRNAs were designed using the Benchling CRISPR gRNA Design tool (www.benchling.com) and cloned into the LentiCRISPRv2 vector expressing Streptococcus pyogenes Cas9 (spCas9) (Addgene #52961). .. Cloning involved annealed and phosphorylated oligonucleotides (Sigma-Aldrich) targeting specific sequences, with transformations conducted in Stbl3 bacteria (Thermo Fisher Scientific).



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