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genome-wide crispr activation screen  (Broad Institute Inc)

 
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    Broad Institute Inc genome-wide crispr activation screen
    Genome Wide Crispr Activation Screen, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/crispr+activation+screen/crispr+screens/pmc11001640__mmc4-1-0-52
    Average 90 stars, based on 1 article reviews
    genome-wide crispr activation screen - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    CRISPR:

    Article Title: CRISPR activation screen identifies BCL-2 proteins and B3GNT2 as drivers of cancer resistance to T cell-mediated cytotoxicity
    Article Snippet: 1 Department of Biological Engineering, MIT, Cambridge, MA 02139, USA 2 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 3 Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA 4 McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA 5 Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA 6 Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA 7 Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA 8 Present address: Whitehead Institute, Cambridge, MA 02142, USA .. Supplementary Information CRISPR activation screen identifies BCL-2 proteins and B3GNT2 as drivers of cancer resistance to T cell-mediated cytotoxicity Julia Joung1,2,3,4,5,8,†, Paul C. Kirchgatterer1,2,3,4,5, Ankita Singh1,2,3,4,5, Jang H. Cho1,2,3,4,5, Suchita P. Nety1,2,3,4,5, Rebecca C. Larson6,7, Rhiannon K. Macrae1,2,3,4,5, Rebecca Deasy2, Yuen-Yi Tseng2, Marcela V. Maus6,7, and Feng Zhang1,2,3,4,5,† 1 Department of Biological Engineering, MIT, Cambridge, MA 02139, USA 2 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 3 Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA 4 McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA 5 Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA 6 Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA 7 Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA 8 Present address: Whitehead Institute, Cambridge, MA 02142, USA † Correspondence should be addressed to julia@joung.science (J.J.) and zhang@broadinstitute.org (F.Z.). ..

    Article Title: Identification of regulators of poly-ADP-ribose polymerase (PARP) inhibitor response through complementary CRISPR knockout and activation screens
    Article Snippet: .. For the CRISPR activation screen, HeLa BRCA2-knockout cells were infected with dCas9 (Addgene, 61425-LV) and selected with blasticidin (3 μg/ml). dCas9-expressing cells were then transduced with the Calabrese Human CRISPR Activation Pooled Library (Set A, Addgene, 92379-LV) using enough cells to obtain a library coverage of 500 cells per sgRNA at an MOI of 0.4. ..

    Activation Assay:

    Article Title: CRISPR activation screen identifies BCL-2 proteins and B3GNT2 as drivers of cancer resistance to T cell-mediated cytotoxicity
    Article Snippet: 1 Department of Biological Engineering, MIT, Cambridge, MA 02139, USA 2 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 3 Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA 4 McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA 5 Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA 6 Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA 7 Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA 8 Present address: Whitehead Institute, Cambridge, MA 02142, USA .. Supplementary Information CRISPR activation screen identifies BCL-2 proteins and B3GNT2 as drivers of cancer resistance to T cell-mediated cytotoxicity Julia Joung1,2,3,4,5,8,†, Paul C. Kirchgatterer1,2,3,4,5, Ankita Singh1,2,3,4,5, Jang H. Cho1,2,3,4,5, Suchita P. Nety1,2,3,4,5, Rebecca C. Larson6,7, Rhiannon K. Macrae1,2,3,4,5, Rebecca Deasy2, Yuen-Yi Tseng2, Marcela V. Maus6,7, and Feng Zhang1,2,3,4,5,† 1 Department of Biological Engineering, MIT, Cambridge, MA 02139, USA 2 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 3 Department of Brain and Cognitive Science, MIT, Cambridge, MA 02139, USA 4 McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA 5 Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA 6 Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA 7 Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA 8 Present address: Whitehead Institute, Cambridge, MA 02142, USA † Correspondence should be addressed to julia@joung.science (J.J.) and zhang@broadinstitute.org (F.Z.). ..

    Article Title: Identification of regulators of poly-ADP-ribose polymerase (PARP) inhibitor response through complementary CRISPR knockout and activation screens
    Article Snippet: .. For the CRISPR activation screen, HeLa BRCA2-knockout cells were infected with dCas9 (Addgene, 61425-LV) and selected with blasticidin (3 μg/ml). dCas9-expressing cells were then transduced with the Calabrese Human CRISPR Activation Pooled Library (Set A, Addgene, 92379-LV) using enough cells to obtain a library coverage of 500 cells per sgRNA at an MOI of 0.4. ..

    Infection:

    Article Title: Identification of regulators of poly-ADP-ribose polymerase (PARP) inhibitor response through complementary CRISPR knockout and activation screens
    Article Snippet: .. For the CRISPR activation screen, HeLa BRCA2-knockout cells were infected with dCas9 (Addgene, 61425-LV) and selected with blasticidin (3 μg/ml). dCas9-expressing cells were then transduced with the Calabrese Human CRISPR Activation Pooled Library (Set A, Addgene, 92379-LV) using enough cells to obtain a library coverage of 500 cells per sgRNA at an MOI of 0.4. ..

    Transduction:

    Article Title: Identification of regulators of poly-ADP-ribose polymerase (PARP) inhibitor response through complementary CRISPR knockout and activation screens
    Article Snippet: .. For the CRISPR activation screen, HeLa BRCA2-knockout cells were infected with dCas9 (Addgene, 61425-LV) and selected with blasticidin (3 μg/ml). dCas9-expressing cells were then transduced with the Calabrese Human CRISPR Activation Pooled Library (Set A, Addgene, 92379-LV) using enough cells to obtain a library coverage of 500 cells per sgRNA at an MOI of 0.4. ..

    Genome Wide:

    Article Title: Genome-wide CRISPR activation screen identifies JADE3 as an antiviral activator of NF-kB
    Article Snippet: 1 Departments of Immunology and Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA 2 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 3 Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA 4 Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA 5 Departments of Laboratory Medicine and Immunobiology, Yale School of Medicine, New Haven, CT, USA # Correspondence to: Robert.Orchard@UTSouthwestern.edu .. SUPPLEMENTAL INFORMATION APPENDIX Genome-wide CRISPR activation screen identifies JADE3 as an antiviral activator of NF-kB Moiz Munir1, Aaron Embry1, John G. Doench2, Peter Palese3, Nicholas S. Heaton4, Craig B. Wilen5, Robert C. Orchard1# 1 Departments of Immunology and Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, USA 2 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 3 Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, ..



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    genome-wide crispr activation screen  (Broad Institute Inc)
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    Receptor-ligand <t>CRISPR-Cas9</t> activation screen reveals that CD55 interacts with HLA-C∗07:01-VRIG tetramers (A) Schematic of the receptor ligand CRISPR-Cas9 activation screen. K562 cells transduced with a genome-wide activation library were stained with a pool of three HLA tetramers (HLA-A∗02:01-NLVP, HLA-B∗07:02-TPRV, and HLA-C∗07:01-VRIG), and enriched gRNAs in stained cells were identified using NGS. (B) SigmaFC scores of genes from two replicate screens. SigmaFC scores were calculated using PinAplPy, and top hits are annotated. (C) K562 cells stably expressing dCas9 and transduced with a gRNA upregulating CD55 or a control guide were stained with the HLA-A, -B, -C, or tetramers as in (A) or with HLA-E∗01:01-VMAP tetramers and analyzed by flow cytometry. (D) In vitro co-immunoprecipitation of recombinant CD55-Fc with HLA-A∗02:01-NLVP, HLA-B∗07:02-TPRV, HLA-C∗07:01-VRIG, or HLA-E∗01:01-VMAP tetramers. (E) Three different cell lines (HeLa, PC-3M, or SiHa) that express CD55 endogenously were stained for CD55 (top) or with HLA-C∗07:01-VRIG tetramers (bottom) and analyzed by flow cytometry. (F) HeLa wild-type or HeLa CD55 KO cells were stained with αCD55 or HLA-C∗07:01-VRIG tetramers and analyzed by flow cytometry. All data except (B) represent at least three independent experiments. <t>CRISPRa,</t> CRISPR activation screen; TMs, tetramers; WT, wild-type; KO, knockout. Related to <xref ref-type=Figure S1 and Table S1 . " width="250" height="auto" />
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    Image Search Results


    (A) Schematic overview of the receptor-ligand CRISPR activation screen. K562 cells stably expressing dCas9 were transduced with a genome-wide activation library and stained with a pool of HLA-E*01:03 tetramers loaded with 4 different peptides (VLRPGGHFL, RMPPLGHEL, VMAPRTLIL, RLPAKAPLL). Enrichment of gRNAs in sorted cell populations were determined using next generation sequencing. (B) Gene ranking scores of genes in two replicate screens were calculated using SigmaFC scores from PinAPL-Py and plotted against each other. Hits of interest are annotated. (C) Enrichment of single gRNAs for top hits of the screen, red and blue stripes represent enrichment of individual gRNAs of two replicate sorts compared to unsorted cells. (D) K562 dCas9 cells were transduced with a control guide or a gRNA upregulating either STAB1 or STAB2, stained with HLA-A, -B, -C or -E tetramers (HLA-A*02:01 NLVPMVATV, HLA-B*07:02 TPRVTGGGAM, HLA-C*07:01-VRIGHLYIL, HLA-E*01:03 RMPPLGHEL) and analysed by flow cytometry. (E) K562 gSTAB1 or K562 gSTAB2 cells were stained with HLA tetramers (HLA-A*02:01; HLA-B*07:02; HLA-E*01:03) loaded with indicated peptides and analysed by flow cytometry. All graphs represent at least two biological replicates.

    Journal: PLOS One

    Article Title: Conformation of HLA-E/peptide complex guides interaction with two novel HLA-E receptors: Stabilin 1 and 2

    doi: 10.1371/journal.pone.0334543

    Figure Lengend Snippet: (A) Schematic overview of the receptor-ligand CRISPR activation screen. K562 cells stably expressing dCas9 were transduced with a genome-wide activation library and stained with a pool of HLA-E*01:03 tetramers loaded with 4 different peptides (VLRPGGHFL, RMPPLGHEL, VMAPRTLIL, RLPAKAPLL). Enrichment of gRNAs in sorted cell populations were determined using next generation sequencing. (B) Gene ranking scores of genes in two replicate screens were calculated using SigmaFC scores from PinAPL-Py and plotted against each other. Hits of interest are annotated. (C) Enrichment of single gRNAs for top hits of the screen, red and blue stripes represent enrichment of individual gRNAs of two replicate sorts compared to unsorted cells. (D) K562 dCas9 cells were transduced with a control guide or a gRNA upregulating either STAB1 or STAB2, stained with HLA-A, -B, -C or -E tetramers (HLA-A*02:01 NLVPMVATV, HLA-B*07:02 TPRVTGGGAM, HLA-C*07:01-VRIGHLYIL, HLA-E*01:03 RMPPLGHEL) and analysed by flow cytometry. (E) K562 gSTAB1 or K562 gSTAB2 cells were stained with HLA tetramers (HLA-A*02:01; HLA-B*07:02; HLA-E*01:03) loaded with indicated peptides and analysed by flow cytometry. All graphs represent at least two biological replicates.

    Article Snippet: CRISPR activation screens were performed by transducing K562 cells with dCas9-Blast (Addgene #61425), a kind gift from Feng Zhang, and the Calabrese genome-wide activation library (sublibrary A + B), kindly provided by John Doench (Addgene # 1000000111).

    Techniques: CRISPR, Activation Assay, Stable Transfection, Expressing, Transduction, Genome Wide, Staining, Next-Generation Sequencing, Control, Flow Cytometry

    Receptor-ligand CRISPR-Cas9 activation screen reveals that CD55 interacts with HLA-C∗07:01-VRIG tetramers (A) Schematic of the receptor ligand CRISPR-Cas9 activation screen. K562 cells transduced with a genome-wide activation library were stained with a pool of three HLA tetramers (HLA-A∗02:01-NLVP, HLA-B∗07:02-TPRV, and HLA-C∗07:01-VRIG), and enriched gRNAs in stained cells were identified using NGS. (B) SigmaFC scores of genes from two replicate screens. SigmaFC scores were calculated using PinAplPy, and top hits are annotated. (C) K562 cells stably expressing dCas9 and transduced with a gRNA upregulating CD55 or a control guide were stained with the HLA-A, -B, -C, or tetramers as in (A) or with HLA-E∗01:01-VMAP tetramers and analyzed by flow cytometry. (D) In vitro co-immunoprecipitation of recombinant CD55-Fc with HLA-A∗02:01-NLVP, HLA-B∗07:02-TPRV, HLA-C∗07:01-VRIG, or HLA-E∗01:01-VMAP tetramers. (E) Three different cell lines (HeLa, PC-3M, or SiHa) that express CD55 endogenously were stained for CD55 (top) or with HLA-C∗07:01-VRIG tetramers (bottom) and analyzed by flow cytometry. (F) HeLa wild-type or HeLa CD55 KO cells were stained with αCD55 or HLA-C∗07:01-VRIG tetramers and analyzed by flow cytometry. All data except (B) represent at least three independent experiments. CRISPRa, CRISPR activation screen; TMs, tetramers; WT, wild-type; KO, knockout. Related to <xref ref-type=Figure S1 and Table S1 . " width="100%" height="100%">

    Journal: iScience

    Article Title: CRISPR-Cas9 screening reveals a distinct class of MHC-I binders with precise HLA-peptide recognition

    doi: 10.1016/j.isci.2024.110120

    Figure Lengend Snippet: Receptor-ligand CRISPR-Cas9 activation screen reveals that CD55 interacts with HLA-C∗07:01-VRIG tetramers (A) Schematic of the receptor ligand CRISPR-Cas9 activation screen. K562 cells transduced with a genome-wide activation library were stained with a pool of three HLA tetramers (HLA-A∗02:01-NLVP, HLA-B∗07:02-TPRV, and HLA-C∗07:01-VRIG), and enriched gRNAs in stained cells were identified using NGS. (B) SigmaFC scores of genes from two replicate screens. SigmaFC scores were calculated using PinAplPy, and top hits are annotated. (C) K562 cells stably expressing dCas9 and transduced with a gRNA upregulating CD55 or a control guide were stained with the HLA-A, -B, -C, or tetramers as in (A) or with HLA-E∗01:01-VMAP tetramers and analyzed by flow cytometry. (D) In vitro co-immunoprecipitation of recombinant CD55-Fc with HLA-A∗02:01-NLVP, HLA-B∗07:02-TPRV, HLA-C∗07:01-VRIG, or HLA-E∗01:01-VMAP tetramers. (E) Three different cell lines (HeLa, PC-3M, or SiHa) that express CD55 endogenously were stained for CD55 (top) or with HLA-C∗07:01-VRIG tetramers (bottom) and analyzed by flow cytometry. (F) HeLa wild-type or HeLa CD55 KO cells were stained with αCD55 or HLA-C∗07:01-VRIG tetramers and analyzed by flow cytometry. All data except (B) represent at least three independent experiments. CRISPRa, CRISPR activation screen; TMs, tetramers; WT, wild-type; KO, knockout. Related to Figure S1 and Table S1 .

    Article Snippet: For CRISPR activation screening for transmembrane interactors of HLA, K562 cells were transduced with dCAS9-Blast (Addgene #61425), a kind gift from Feng Zhang, and the Calabrese genome-wide activation library (sublibrary A + B), kindly provided by John Doench (Addgene #1000000111).

    Techniques: CRISPR, Activation Assay, Transduction, Genome Wide, Staining, Stable Transfection, Expressing, Control, Flow Cytometry, In Vitro, Immunoprecipitation, Recombinant, Knock-Out

    CRISPR-Cas9 activation and KO screens identify an interaction between HLA-C∗07:02-YRFR and heparan sulfate chains (A) HeLa cells were stained with a variety of HLA-C∗07:02 tetramers loaded with different peptides and analyzed by flow cytometry. (B) The indicated cell lines were stained with HLA-C∗07:02-YRFR tetramers and analyzed by flow cytometry. Staining is normalized to unstained levels of that cell line. (C) Schematic of CRISPR-Cas9 KO screen in MelJuSo cells. Cells were stained with HLA-C∗07:02-YRFR, and enriched gRNAs in non-binding cells were identified using NGS. (D) SigmaFC scores of genes from two replicate screens. SigmaFC scores were calculated using PinAplPy, and genes involved in the heparan sulfate biosynthesis pathway are depicted in purple. Hits used for further validation are annotated. (E) Schematic of the CRISPR-Cas9 activation screen. K562 cells stably expressing dCas9 transduced with a genome-wide activation library were stained with HLA-C YRFR∗07:02 tetramers, and enriched gRNAs in positive cells were identified. (F) SigmaFC scores of genes from two replicate screens. SigmaFC scores were calculated using PinAplPy, and top hits are annotated. Proteoglycans of interest are depicted in purple. CRISPRa, Crispr activation screen. Related to <xref ref-type=Figure S3 , Table S1 and . " width="100%" height="100%">

    Journal: iScience

    Article Title: CRISPR-Cas9 screening reveals a distinct class of MHC-I binders with precise HLA-peptide recognition

    doi: 10.1016/j.isci.2024.110120

    Figure Lengend Snippet: CRISPR-Cas9 activation and KO screens identify an interaction between HLA-C∗07:02-YRFR and heparan sulfate chains (A) HeLa cells were stained with a variety of HLA-C∗07:02 tetramers loaded with different peptides and analyzed by flow cytometry. (B) The indicated cell lines were stained with HLA-C∗07:02-YRFR tetramers and analyzed by flow cytometry. Staining is normalized to unstained levels of that cell line. (C) Schematic of CRISPR-Cas9 KO screen in MelJuSo cells. Cells were stained with HLA-C∗07:02-YRFR, and enriched gRNAs in non-binding cells were identified using NGS. (D) SigmaFC scores of genes from two replicate screens. SigmaFC scores were calculated using PinAplPy, and genes involved in the heparan sulfate biosynthesis pathway are depicted in purple. Hits used for further validation are annotated. (E) Schematic of the CRISPR-Cas9 activation screen. K562 cells stably expressing dCas9 transduced with a genome-wide activation library were stained with HLA-C YRFR∗07:02 tetramers, and enriched gRNAs in positive cells were identified. (F) SigmaFC scores of genes from two replicate screens. SigmaFC scores were calculated using PinAplPy, and top hits are annotated. Proteoglycans of interest are depicted in purple. CRISPRa, Crispr activation screen. Related to Figure S3 , Table S1 and .

    Article Snippet: For CRISPR activation screening for transmembrane interactors of HLA, K562 cells were transduced with dCAS9-Blast (Addgene #61425), a kind gift from Feng Zhang, and the Calabrese genome-wide activation library (sublibrary A + B), kindly provided by John Doench (Addgene #1000000111).

    Techniques: CRISPR, Activation Assay, Staining, Flow Cytometry, Binding Assay, Biomarker Discovery, Stable Transfection, Expressing, Transduction, Genome Wide

    Journal: iScience

    Article Title: CRISPR-Cas9 screening reveals a distinct class of MHC-I binders with precise HLA-peptide recognition

    doi: 10.1016/j.isci.2024.110120

    Figure Lengend Snippet:

    Article Snippet: For CRISPR activation screening for transmembrane interactors of HLA, K562 cells were transduced with dCAS9-Blast (Addgene #61425), a kind gift from Feng Zhang, and the Calabrese genome-wide activation library (sublibrary A + B), kindly provided by John Doench (Addgene #1000000111).

    Techniques: Virus, Recombinant, Blocking Assay, Genome Wide, Activation Assay, CRISPR, Knock-Out, Mutagenesis, Plasmid Preparation, Software, Imaging