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crispr cas9 knockout cell lines  (Addgene inc)


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    Structured Review

    Addgene inc crispr cas9 knockout cell lines
    Crispr Cas9 Knockout Cell Lines, supplied by Addgene inc, used in various techniques. Bioz Stars score: 96/100, based on 6234 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/cas9/lentiCRISPR+v2+(Plasmid+%2352961)/pmc13693651-166-3-10
    Average 96 stars, based on 6234 article reviews
    crispr cas9 knockout cell lines - by Bioz Stars, 2026-11
    96/100 stars

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    Related Articles

    Expressing:

    Article Title: AcrIIA7 hijacks tracrRNA to block CRISPR-Cas system.
    Article Snippet: .. Additionally, expression constructs for Streptococcus pyogenes Cas9 (#62731), Neisseria meningitides Cas9 (#71474), Haemophilus parainfluenzae Cas9 (#121540), and Simonsiella muelleri Cas9 (#121541) were procured from Addgene. ..

    Construct:

    Article Title: AcrIIA7 hijacks tracrRNA to block CRISPR-Cas system.
    Article Snippet: .. Additionally, expression constructs for Streptococcus pyogenes Cas9 (#62731), Neisseria meningitides Cas9 (#71474), Haemophilus parainfluenzae Cas9 (#121540), and Simonsiella muelleri Cas9 (#121541) were procured from Addgene. ..

    Article Title: Cohesin and its regulation promote monopolar kinetochore orientation at meiosis I in Arabidopsis.
    Article Snippet: The complete assembly into the final destination vector pAGM4723 (Addgene #48015) was performed using a Bpi-based Golden Gate reaction. .. The construct incorporated the FAST-Red clone (Addgene #117499; pICSL11015) as a seed coat selection marker at position 1, followed by the Cas9 clone (Addgene #153224; pAGM51323), carrying an enhanced SpCas9 driven by the AtRPS5 promoter, at position 2. ..

    Article Title: Compositions and methods for targeted delivery of CRISPR-Cas effector polypeptides and transgenes
    Article Snippet: Plasmid Construction The Gag-pol expression plasmid psPax2 was a gift from Didier Trono (Addgene plasmid #12260). pCMV-VSV-G was a gift from Bob Weinberg (Addgene plasmid #8454). .. Gag-Cas9 was constructed by amplifying Gag from psPax2 and Cas9 from pMJ920 (Addgene plasmid #42234). .. HIV-1 Env amino acid sequence was obtained from UniProt (P04578), human codon optimized (IDT), and ordered as a gBlock (IDT).

    Selection:

    Article Title: Cohesin and its regulation promote monopolar kinetochore orientation at meiosis I in Arabidopsis.
    Article Snippet: The complete assembly into the final destination vector pAGM4723 (Addgene #48015) was performed using a Bpi-based Golden Gate reaction. .. The construct incorporated the FAST-Red clone (Addgene #117499; pICSL11015) as a seed coat selection marker at position 1, followed by the Cas9 clone (Addgene #153224; pAGM51323), carrying an enhanced SpCas9 driven by the AtRPS5 promoter, at position 2. ..

    Marker:

    Article Title: Cohesin and its regulation promote monopolar kinetochore orientation at meiosis I in Arabidopsis.
    Article Snippet: The complete assembly into the final destination vector pAGM4723 (Addgene #48015) was performed using a Bpi-based Golden Gate reaction. .. The construct incorporated the FAST-Red clone (Addgene #117499; pICSL11015) as a seed coat selection marker at position 1, followed by the Cas9 clone (Addgene #153224; pAGM51323), carrying an enhanced SpCas9 driven by the AtRPS5 promoter, at position 2. ..

    Transduction:


    Plasmid Preparation:


    Article Title: SMCHD1 is a target for gene activation therapy to treat Prader-Willi syndrome
    Article Snippet: Guide RNA (gRNAs) were cloned into lentiGuide-Puro (Addgene #52963) and pFgH1UTPuro (Addgene #70183 with the GFP reporter replaced by puromycin resistance). .. HEK293T cells at 80% confluency were transfected via calcium phosphate-mediated transfection with the psPAX packaging vector, the VSVg envelope vector, and a plasmid containing either a SMCHD1 gRNA or Cas9 (Addgene #52962) in the ratio of 2.5:1:1.5. ..

    Article Title: Engineered human iPS cell models reveal altered podocytogenesis in congenital heart disease-associated SMAD2 mutations
    Article Snippet: .. SMAD2 loss-of-function iPS cells were generated by non-homologous end joining (NHEJ) as previously described 107 Two micrograms of plasmid-expressing Cas9 (PX459v2 from Addgene) were co-transfected with 2 μg plasmid-expressing guide RNA using a stem cell nucleofector kit (Lonza, Amaxa). ..

    Article Title: Compositions and methods for targeted delivery of CRISPR-Cas effector polypeptides and transgenes
    Article Snippet: Plasmid Construction The Gag-pol expression plasmid psPax2 was a gift from Didier Trono (Addgene plasmid #12260). pCMV-VSV-G was a gift from Bob Weinberg (Addgene plasmid #8454). .. Gag-Cas9 was constructed by amplifying Gag from psPax2 and Cas9 from pMJ920 (Addgene plasmid #42234). .. HIV-1 Env amino acid sequence was obtained from UniProt (P04578), human codon optimized (IDT), and ordered as a gBlock (IDT).

    Transfection:

    Article Title: SMCHD1 is a target for gene activation therapy to treat Prader-Willi syndrome
    Article Snippet: Guide RNA (gRNAs) were cloned into lentiGuide-Puro (Addgene #52963) and pFgH1UTPuro (Addgene #70183 with the GFP reporter replaced by puromycin resistance). .. HEK293T cells at 80% confluency were transfected via calcium phosphate-mediated transfection with the psPAX packaging vector, the VSVg envelope vector, and a plasmid containing either a SMCHD1 gRNA or Cas9 (Addgene #52962) in the ratio of 2.5:1:1.5. ..

    Generated:

    Article Title: Engineered human iPS cell models reveal altered podocytogenesis in congenital heart disease-associated SMAD2 mutations
    Article Snippet: .. SMAD2 loss-of-function iPS cells were generated by non-homologous end joining (NHEJ) as previously described 107 Two micrograms of plasmid-expressing Cas9 (PX459v2 from Addgene) were co-transfected with 2 μg plasmid-expressing guide RNA using a stem cell nucleofector kit (Lonza, Amaxa). ..

    Non-Homologous End Joining:

    Article Title: Engineered human iPS cell models reveal altered podocytogenesis in congenital heart disease-associated SMAD2 mutations
    Article Snippet: .. SMAD2 loss-of-function iPS cells were generated by non-homologous end joining (NHEJ) as previously described 107 Two micrograms of plasmid-expressing Cas9 (PX459v2 from Addgene) were co-transfected with 2 μg plasmid-expressing guide RNA using a stem cell nucleofector kit (Lonza, Amaxa). ..

    Stem Cell:

    Article Title: Engineered human iPS cell models reveal altered podocytogenesis in congenital heart disease-associated SMAD2 mutations
    Article Snippet: .. SMAD2 loss-of-function iPS cells were generated by non-homologous end joining (NHEJ) as previously described 107 Two micrograms of plasmid-expressing Cas9 (PX459v2 from Addgene) were co-transfected with 2 μg plasmid-expressing guide RNA using a stem cell nucleofector kit (Lonza, Amaxa). ..



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    Image Search Results


    ( A ) Volcano plot showing dysregulated genes in lung adenocarcinoma tumors (TCGA-LUAD cohort) carrying driver mutations in NFE2L2 or KEAP1 [cutoffs: Log2(FC) = ±0.6 and P -adj ≤ 0.05]. ( B ) Gene Set Enrichment Analysis (GSEA) using Kyoto Encyclopedia of Genes and Genomes (KEGG) gene sets in the TCGA-LUAD cohort with mutations in NFE2L2 or KEAP1 . ( C ) mRNA expression of selected genes involved in formaldehyde (FA) detoxification in KEAP1-NFE2L2 mutated and nonmutated (WT) LUAD tumors. ( D ) mRNA expression of selected genes in normal lung and whole blood obtained from GTEX. ( E ) Single-cell RNA-seq data from mouse hematopoietic and progenitor cells (HPC) plotted with kleintools ( https://kleintools.hms.harvard.edu/tools/spring.html ) . ( F ) Representative images of Western blots of selected factors from (A) performed in different cell lines. ( G ) Cystine uptake assay performed in selected cell lines (mean ± SEM, n = 3). ( H ) FA tolerance of A549 cells lacking SLC7A11 (sg SLC7A11 ) complemented with a wild-type copy of SLC7A11 (pSLC7A11) grown in the presence of 100 μM BSO (mean ± SEM, n = 3 and two-way ANOVA, **** P < 0.0001). ( I ) FA tolerance for H1299 cells harboring empty vector (pEV) or pSLC7A11 in the presence of 100 μM BSO [mean ± SEM, n = 3 and two-way ANOVA (Tukey test between untreated (UT) and BSO at each point); for H1299 pEV: **** P < 0.0001 and *** P = 0.0002]. ( J ) Viability of A549 cells carrying sg SLC7A11 and sgNTC (nontargeting control) under cystine deprivation [one-way ANOVA (Tukey test)]. ( K ) Glutathione (GSH) levels of the indicated cell lines maintained during 48 hours under cystine deprivation and exposing to FA during the last 24 hours [one-way ANOVA (Tukey test), ** P = 0.0058]. ( L ) FA tolerance of A549 cells lacking ADH5 in the presence of BSO (100 μM) or ERA (5 μM) [mean ± SEM, n = 6 and two-way ANOVA (Tukey test between UT and BSO or ERA at each point for multiple comparison); * P = 0.0300 and **** P < 0.0001].

    Journal: Science Advances

    Article Title: NRF2 coordinates cystine import and glutathione use to sustain ferroptosis resistance and formaldehyde tolerance in cancer

    doi: 10.1126/sciadv.aea1431

    Figure Lengend Snippet: ( A ) Volcano plot showing dysregulated genes in lung adenocarcinoma tumors (TCGA-LUAD cohort) carrying driver mutations in NFE2L2 or KEAP1 [cutoffs: Log2(FC) = ±0.6 and P -adj ≤ 0.05]. ( B ) Gene Set Enrichment Analysis (GSEA) using Kyoto Encyclopedia of Genes and Genomes (KEGG) gene sets in the TCGA-LUAD cohort with mutations in NFE2L2 or KEAP1 . ( C ) mRNA expression of selected genes involved in formaldehyde (FA) detoxification in KEAP1-NFE2L2 mutated and nonmutated (WT) LUAD tumors. ( D ) mRNA expression of selected genes in normal lung and whole blood obtained from GTEX. ( E ) Single-cell RNA-seq data from mouse hematopoietic and progenitor cells (HPC) plotted with kleintools ( https://kleintools.hms.harvard.edu/tools/spring.html ) . ( F ) Representative images of Western blots of selected factors from (A) performed in different cell lines. ( G ) Cystine uptake assay performed in selected cell lines (mean ± SEM, n = 3). ( H ) FA tolerance of A549 cells lacking SLC7A11 (sg SLC7A11 ) complemented with a wild-type copy of SLC7A11 (pSLC7A11) grown in the presence of 100 μM BSO (mean ± SEM, n = 3 and two-way ANOVA, **** P < 0.0001). ( I ) FA tolerance for H1299 cells harboring empty vector (pEV) or pSLC7A11 in the presence of 100 μM BSO [mean ± SEM, n = 3 and two-way ANOVA (Tukey test between untreated (UT) and BSO at each point); for H1299 pEV: **** P < 0.0001 and *** P = 0.0002]. ( J ) Viability of A549 cells carrying sg SLC7A11 and sgNTC (nontargeting control) under cystine deprivation [one-way ANOVA (Tukey test)]. ( K ) Glutathione (GSH) levels of the indicated cell lines maintained during 48 hours under cystine deprivation and exposing to FA during the last 24 hours [one-way ANOVA (Tukey test), ** P = 0.0058]. ( L ) FA tolerance of A549 cells lacking ADH5 in the presence of BSO (100 μM) or ERA (5 μM) [mean ± SEM, n = 6 and two-way ANOVA (Tukey test between UT and BSO or ERA at each point for multiple comparison); * P = 0.0300 and **** P < 0.0001].

    Article Snippet: ADH5 -deficient cells were generated in A549 cells stably expressing Cas9 (Addgene, catalog no. 78546) infected with a lentiviral vector coding for an sgRNA against the exon 3 of ADH 5 previously published ( ).

    Techniques: Analysis, Expressing, Single Cell, RNA Sequencing, Western Blot, Plasmid Preparation, Control, Comparison

    a , Top: DO1Cas9 CRISPR–Cas locus. Bottom: RNA secondary structure (predicted using trRosettaRNA ) and sequence of a DO1Cas9 sgRNA, consisting of a 20-nt variable region (green) matching a target sequence upstream of the PAM, followed by repeat (orange) and tracrRNA (blue) sequences connected by a linker (purple). b , Cleavage activity of DO1Cas9 and SpCas9, synthesized by in vitro transcription-translation (IVTT), at varying dilutions (10×, 100×, 1000×) on a PAM library. Bands indicate PCR-amplified adapter-ligated cut fragments . c , Left: WebLogo of PAM preferences from position frequency matrices (PFMs) of DO1Cas9 (100nM, 100× dilution) cut sites in a plasmid library Right: nucleotide permissiveness within the 7-nucleotide PAM region (green, full; yellow, moderate; orange, low; red, none). d , Phylogenetic tree of Cas9 nucleases generated using iTOL (Interactive Tree of Life) from sequences retrieved from the Caspedia Database and the Malaspina Dataset , colored by Class 2 type (II-A, II-B, II-C). e , DO1Cas9 structure modeled with AlphaFold. f , Local structural flexibility (RMSF) for DO1Cas9, SpCas9, and GeoCas9 AlphaFold models. g , Predicted free energy of unfolding (kcal/mol) for the same three proteins. h , Unfolding dynamics for DO1Cas9 and SpCas9 ± gRNA, by nanoDSF. i , Top: pipeline testing how temperature pre-treatment of DO1Cas9 and SpCas9 apo-forms affects subsequent RNP nuclease activity. Bottom: in vitro nuclease activity of DO1Cas9 and SpCas9 RNPs after incubating the apo-forms at different temperatures for 1h. j , Top: scheme of capillary electrophoresis-based fragment analysis. Bottom: percentage of DNA cleavage by DO1Cas9 across 15–40°C (mean ± SD, N = 3). k , Left: setup for low temperature digestions. Middle: in vitro digestion by DO1Cas9 and SpCas9 RNPs at low (7.6°C, 120 min) and moderate (20°C, 30 min) temperatures. Right: percentage of DNA cleavage by DO1Cas9 and SpCas9 at ∼7.6°C at different timepoints, analyzed by capillary electrophoresis (mean ± s.d.; DO1Cas9, N = 3; SpCas9, N = 2). l , In vitro digestion of gfp PCR amplicons by DO1Cas9 and SpCas9 using gRNAs with a perfectly matched spacer (M) or with mismatches at positions +1, +3, and +5. C, undigested control.

    Journal: bioRxiv

    Article Title: A cold-adapted Cas9 nuclease from the deep ocean

    doi: 10.64898/2026.10.14.759226

    Figure Lengend Snippet: a , Top: DO1Cas9 CRISPR–Cas locus. Bottom: RNA secondary structure (predicted using trRosettaRNA ) and sequence of a DO1Cas9 sgRNA, consisting of a 20-nt variable region (green) matching a target sequence upstream of the PAM, followed by repeat (orange) and tracrRNA (blue) sequences connected by a linker (purple). b , Cleavage activity of DO1Cas9 and SpCas9, synthesized by in vitro transcription-translation (IVTT), at varying dilutions (10×, 100×, 1000×) on a PAM library. Bands indicate PCR-amplified adapter-ligated cut fragments . c , Left: WebLogo of PAM preferences from position frequency matrices (PFMs) of DO1Cas9 (100nM, 100× dilution) cut sites in a plasmid library Right: nucleotide permissiveness within the 7-nucleotide PAM region (green, full; yellow, moderate; orange, low; red, none). d , Phylogenetic tree of Cas9 nucleases generated using iTOL (Interactive Tree of Life) from sequences retrieved from the Caspedia Database and the Malaspina Dataset , colored by Class 2 type (II-A, II-B, II-C). e , DO1Cas9 structure modeled with AlphaFold. f , Local structural flexibility (RMSF) for DO1Cas9, SpCas9, and GeoCas9 AlphaFold models. g , Predicted free energy of unfolding (kcal/mol) for the same three proteins. h , Unfolding dynamics for DO1Cas9 and SpCas9 ± gRNA, by nanoDSF. i , Top: pipeline testing how temperature pre-treatment of DO1Cas9 and SpCas9 apo-forms affects subsequent RNP nuclease activity. Bottom: in vitro nuclease activity of DO1Cas9 and SpCas9 RNPs after incubating the apo-forms at different temperatures for 1h. j , Top: scheme of capillary electrophoresis-based fragment analysis. Bottom: percentage of DNA cleavage by DO1Cas9 across 15–40°C (mean ± SD, N = 3). k , Left: setup for low temperature digestions. Middle: in vitro digestion by DO1Cas9 and SpCas9 RNPs at low (7.6°C, 120 min) and moderate (20°C, 30 min) temperatures. Right: percentage of DNA cleavage by DO1Cas9 and SpCas9 at ∼7.6°C at different timepoints, analyzed by capillary electrophoresis (mean ± s.d.; DO1Cas9, N = 3; SpCas9, N = 2). l , In vitro digestion of gfp PCR amplicons by DO1Cas9 and SpCas9 using gRNAs with a perfectly matched spacer (M) or with mismatches at positions +1, +3, and +5. C, undigested control.

    Article Snippet: Unless otherwise indicated, ribonucleoprotein (RNP) complexes were assembled by incubating purified Cas9 protein (350 nM) and sgRNA (350 nM) in 1× NEBuffer r3.1 (NEB, B7203S) in a final volume of 30 μl for 30 min at 20 °C.

    Techniques: CRISPR, Sequencing, Activity Assay, Synthesized, In Vitro, Amplification, Plasmid Preparation, Generated, Nano Differential Scanning Fluorimetry, Capillary Electrophoresis, Analysis, Control