perturb seq guide barcode gbc library (Addgene inc)

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Addgene inc perturb seq guide barcode gbc library
Perturb Seq Guide Barcode Gbc Library, supplied by Addgene inc, used in various techniques. Bioz Stars score: 92/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/barcoding/Perturb-seq+Guide+Barcodes+(GBC)+Library+(Pooled+Library+%2385968)/pmc12680425-84-4-9
Average 92 stars, based on 12 article reviews

perturb seq guide barcode gbc library - by Bioz Stars, 2026-09

92/100 stars

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Sequencing:

Article Title: Focal adhesion kinase-YAP signaling axis drives drug-tolerant persister cells and residual disease in lung cancer.
Article Snippet: .. This allowed for a substantial search space ( ~ 2.6e + 33 possible daughter cells) and provided a reasonable model system for studying stochastically determined cell group fates. scRNA sequencing trajectory A BFP-tagged barcode library (Addgene #85968) was delivered via lentiviral infection into isogenic EGFR-mutant PC9-C2 and H1975-B10 cells. ..

Article Title: Focal adhesion kinase-YAP signaling axis drives drug-tolerant persister cells and residual disease in lung cancer
Article Snippet: .. Gene set enrichment analysis was done using GSEA 4.0.1 software scRNA sequencing trajectory: A BFP-tagged barcode library (Addgene #85968) was delivered via lentiviral infection into isogenic EGFR-mutant PC9-C2 and H1975-B10 cells. ..

Infection:

Article Title: Focal adhesion kinase-YAP signaling axis drives drug-tolerant persister cells and residual disease in lung cancer
Article Snippet: .. A BFP-tagged barcode library (Addgene #85968) was delivered via lentiviral infection into isogenic EGFR-mutant PC9-C2 and H1975-B10 cells. ..

Plasmid Preparation:

Article Title: Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens.
Article Snippet: .. The Perturb-seq vector (pBA439, Addgene #85967) with 18 nucleotide barcode (pBA571, Addgene #85968) was used to generate the BAF subunit-targeting and control guides for the Perturb-seq experiments. .. Barcoded vectors were digested with BstXI (NEB) and BlpI (NEB) to create an insertion site for the 20 nucleotide guide RNA sequences (Table S1).

Article Title: Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-TBP Abcam Cat# Ab51841; RRID: AB_945758 Rabbit monoclonal anti-ARID1A Cell Signaling Technologies Cat# 12354; RRID: AB_2637010 Mouse monoclonal anti-SMARCA4 Santa Cruz Biotechnology Cat# sc-17796; RRID: AB_626762 Rabbit monoclonal anti-SMARCC1 Cell Signaling Technologies Cat# 11956; RRID:AB_2797776 Mouse monoclonal anti-SMARCD1 Santa Cruz Biotechnology Cat# sc-135843; RRID:AB_2192137 Mouse monoclonal anti-FLAG M2 Sigma Aldrich Cat# F1804; RRID:AB_262044 Bacterial and virus strains One Shot Stabl3 Chemically Competent E-coli Invitrogen Cat# C737303 Chemicals, peptides, and recombinant proteins T4 DNA ligase New England Biolabs Cat# M0202L Polyethylenimine (PEI) Thermo Fisher Scientific Cat# NC1014320; CAS: 9002-98-6 T4 PNK New England Biolabs Cat #M0201L Polybrene Fisher Scientific Cat #TR1003G Blasticidin S HCL (10mg/mL) Fisher Scientific Cat #A1113903 Puromycin Dihydrochloride (10mg/mL) Fisher Scientific Cat #A1113803 DMSO Fisher Scientific Cat #BP231-100 EDTA Fisher Scientific Cat #BP2482 BstXI New England Biolabs Cat# R0113S BlpI New England Biolabs Cat# R0585S Critical commercial assays QIAquick Gel Extraction Kit Qiagen Cat #2876X4 MinElute Reaction Cleanup Kit Qiagen Cat# 28206 QIAprep Spin Miniprep Kit Qiagen Cat# 27104 NextSeq 500/550 High output flow cell kit, 150 cycles Illumina Cat# 20024907 MiSeq Reagent Kit v2 Illumina Cat# MS-102-2001 10x Genomics 30 gene expression kit v3 10x Genomics Deposited data Perturb-seq (single and combinatorial) scRNA-seq and SHARE-seq This study GEO: GSE200201 ChIP-seq data 3 GEO: GSE113042 Immunoblot data This study Mendeley: 10.17632/yjypfbb5xf.1 Experimental models: Cell lines HEK 293T LentiX Clontech Fisher Cat #NC9834960 .. Recombinant DNA Perturb-seq vector, pBA439 Dixit et al., 201626 Addgene #85967 18 nt Perturb-seq barcoded vector, pBA571 Dixit et al., 201626 Addgene #85968 mSWI/SNF KO CRISPR Perturb-seq Library This study N/A lentiCas9-Blast Sanjana et al., 201466 Addgene #52962 psPAX2 plasmid Didier Trono Lab Addgene #12260 pMD2.G plasmid Didier Trono Lab Addgene #11259 (Continued on next page) e1 Molecular Cell 83, 1350–1367.e1–e7, April 20, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Code for analyses in this work (perturbseq_baf version 1.0) This study https://doi.org/10.5281/zenodo.7682087 Cellranger version 3.02 Zheng et al.67 https://support.10xgenomics.com/single- cell-gene-expression/software/pipelines/ latest/installation Scanpy version 1.7.2 Wolf et al.68 https://scanpy.readthedocs.io/en/stable/ MIMOSCA Dixit et al.26 https://github.com/asncd/MIMOSCA Scikit learn version 0.24.1 Pedregosa et al.69 https://scikit-learn.org/stable/index.html Goatools 1.1.6 Klopfenstein et al.70 https://github.com/tanghaibao/goatools SHARE-seq-alignment Ma et al.42 https://github.com/masai1116/SHARE- seq-alignment MACS2 version 2.2.7.1 Zhang et al.71 https://github.com/macs3-project/MACS Seurat version 4.0.4 Hao et al.72 https://satijalab.org/seurat/ Signac version 1.3.0 Stuart et al.73 https://stuartlab.org/signac/ ChromVAR version 1.14.0 Schep et al.74 https://greenleaflab.github.io/chromVAR/ index.html Geosketch version 1.2 Hie et al.75 https://github.com/brianhie/geosketch Other GlutaMAX Supplement Fisher Scientific Cat# 35-050-061 Non-essential Amino Acids Solution (100X) Fisher Scientific Cat# 11-140-050 Sodium Pyruvate (100 mM) Fisher Scientific Cat# 11-360-070 HEPES (1M) Fisher Scientific Cat# 15630080 Penicillin-Streptomycin (10,000 U/mL) Fisher Scientific Cat# 15-140-122 RPMI 1640 Thermo Fisher Scientific Cat# 61870036 DMEM high glucose, no glutamine Thermo Fisher Scientific Cat# 11960044 4%-12% Bis-Tris gels Invitrogen Cat# NP0321 Immobilon PVDF Transfer Membrane Millipore Cat# IPVH00010

Control:

Article Title: Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens.
Article Snippet: .. The Perturb-seq vector (pBA439, Addgene #85967) with 18 nucleotide barcode (pBA571, Addgene #85968) was used to generate the BAF subunit-targeting and control guides for the Perturb-seq experiments. .. Barcoded vectors were digested with BstXI (NEB) and BlpI (NEB) to create an insertion site for the 20 nucleotide guide RNA sequences (Table S1).

Software:

Recombinant:

Article Title: Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-TBP Abcam Cat# Ab51841; RRID: AB_945758 Rabbit monoclonal anti-ARID1A Cell Signaling Technologies Cat# 12354; RRID: AB_2637010 Mouse monoclonal anti-SMARCA4 Santa Cruz Biotechnology Cat# sc-17796; RRID: AB_626762 Rabbit monoclonal anti-SMARCC1 Cell Signaling Technologies Cat# 11956; RRID:AB_2797776 Mouse monoclonal anti-SMARCD1 Santa Cruz Biotechnology Cat# sc-135843; RRID:AB_2192137 Mouse monoclonal anti-FLAG M2 Sigma Aldrich Cat# F1804; RRID:AB_262044 Bacterial and virus strains One Shot Stabl3 Chemically Competent E-coli Invitrogen Cat# C737303 Chemicals, peptides, and recombinant proteins T4 DNA ligase New England Biolabs Cat# M0202L Polyethylenimine (PEI) Thermo Fisher Scientific Cat# NC1014320; CAS: 9002-98-6 T4 PNK New England Biolabs Cat #M0201L Polybrene Fisher Scientific Cat #TR1003G Blasticidin S HCL (10mg/mL) Fisher Scientific Cat #A1113903 Puromycin Dihydrochloride (10mg/mL) Fisher Scientific Cat #A1113803 DMSO Fisher Scientific Cat #BP231-100 EDTA Fisher Scientific Cat #BP2482 BstXI New England Biolabs Cat# R0113S BlpI New England Biolabs Cat# R0585S Critical commercial assays QIAquick Gel Extraction Kit Qiagen Cat #2876X4 MinElute Reaction Cleanup Kit Qiagen Cat# 28206 QIAprep Spin Miniprep Kit Qiagen Cat# 27104 NextSeq 500/550 High output flow cell kit, 150 cycles Illumina Cat# 20024907 MiSeq Reagent Kit v2 Illumina Cat# MS-102-2001 10x Genomics 30 gene expression kit v3 10x Genomics Deposited data Perturb-seq (single and combinatorial) scRNA-seq and SHARE-seq This study GEO: GSE200201 ChIP-seq data 3 GEO: GSE113042 Immunoblot data This study Mendeley: 10.17632/yjypfbb5xf.1 Experimental models: Cell lines HEK 293T LentiX Clontech Fisher Cat #NC9834960 .. Recombinant DNA Perturb-seq vector, pBA439 Dixit et al., 201626 Addgene #85967 18 nt Perturb-seq barcoded vector, pBA571 Dixit et al., 201626 Addgene #85968 mSWI/SNF KO CRISPR Perturb-seq Library This study N/A lentiCas9-Blast Sanjana et al., 201466 Addgene #52962 psPAX2 plasmid Didier Trono Lab Addgene #12260 pMD2.G plasmid Didier Trono Lab Addgene #11259 (Continued on next page) e1 Molecular Cell 83, 1350–1367.e1–e7, April 20, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Code for analyses in this work (perturbseq_baf version 1.0) This study https://doi.org/10.5281/zenodo.7682087 Cellranger version 3.02 Zheng et al.67 https://support.10xgenomics.com/single- cell-gene-expression/software/pipelines/ latest/installation Scanpy version 1.7.2 Wolf et al.68 https://scanpy.readthedocs.io/en/stable/ MIMOSCA Dixit et al.26 https://github.com/asncd/MIMOSCA Scikit learn version 0.24.1 Pedregosa et al.69 https://scikit-learn.org/stable/index.html Goatools 1.1.6 Klopfenstein et al.70 https://github.com/tanghaibao/goatools SHARE-seq-alignment Ma et al.42 https://github.com/masai1116/SHARE- seq-alignment MACS2 version 2.2.7.1 Zhang et al.71 https://github.com/macs3-project/MACS Seurat version 4.0.4 Hao et al.72 https://satijalab.org/seurat/ Signac version 1.3.0 Stuart et al.73 https://stuartlab.org/signac/ ChromVAR version 1.14.0 Schep et al.74 https://greenleaflab.github.io/chromVAR/ index.html Geosketch version 1.2 Hie et al.75 https://github.com/brianhie/geosketch Other GlutaMAX Supplement Fisher Scientific Cat# 35-050-061 Non-essential Amino Acids Solution (100X) Fisher Scientific Cat# 11-140-050 Sodium Pyruvate (100 mM) Fisher Scientific Cat# 11-360-070 HEPES (1M) Fisher Scientific Cat# 15630080 Penicillin-Streptomycin (10,000 U/mL) Fisher Scientific Cat# 15-140-122 RPMI 1640 Thermo Fisher Scientific Cat# 61870036 DMEM high glucose, no glutamine Thermo Fisher Scientific Cat# 11960044 4%-12% Bis-Tris gels Invitrogen Cat# NP0321 Immobilon PVDF Transfer Membrane Millipore Cat# IPVH00010

CRISPR:

Article Title: Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal anti-TBP Abcam Cat# Ab51841; RRID: AB_945758 Rabbit monoclonal anti-ARID1A Cell Signaling Technologies Cat# 12354; RRID: AB_2637010 Mouse monoclonal anti-SMARCA4 Santa Cruz Biotechnology Cat# sc-17796; RRID: AB_626762 Rabbit monoclonal anti-SMARCC1 Cell Signaling Technologies Cat# 11956; RRID:AB_2797776 Mouse monoclonal anti-SMARCD1 Santa Cruz Biotechnology Cat# sc-135843; RRID:AB_2192137 Mouse monoclonal anti-FLAG M2 Sigma Aldrich Cat# F1804; RRID:AB_262044 Bacterial and virus strains One Shot Stabl3 Chemically Competent E-coli Invitrogen Cat# C737303 Chemicals, peptides, and recombinant proteins T4 DNA ligase New England Biolabs Cat# M0202L Polyethylenimine (PEI) Thermo Fisher Scientific Cat# NC1014320; CAS: 9002-98-6 T4 PNK New England Biolabs Cat #M0201L Polybrene Fisher Scientific Cat #TR1003G Blasticidin S HCL (10mg/mL) Fisher Scientific Cat #A1113903 Puromycin Dihydrochloride (10mg/mL) Fisher Scientific Cat #A1113803 DMSO Fisher Scientific Cat #BP231-100 EDTA Fisher Scientific Cat #BP2482 BstXI New England Biolabs Cat# R0113S BlpI New England Biolabs Cat# R0585S Critical commercial assays QIAquick Gel Extraction Kit Qiagen Cat #2876X4 MinElute Reaction Cleanup Kit Qiagen Cat# 28206 QIAprep Spin Miniprep Kit Qiagen Cat# 27104 NextSeq 500/550 High output flow cell kit, 150 cycles Illumina Cat# 20024907 MiSeq Reagent Kit v2 Illumina Cat# MS-102-2001 10x Genomics 30 gene expression kit v3 10x Genomics Deposited data Perturb-seq (single and combinatorial) scRNA-seq and SHARE-seq This study GEO: GSE200201 ChIP-seq data 3 GEO: GSE113042 Immunoblot data This study Mendeley: 10.17632/yjypfbb5xf.1 Experimental models: Cell lines HEK 293T LentiX Clontech Fisher Cat #NC9834960 .. Recombinant DNA Perturb-seq vector, pBA439 Dixit et al., 201626 Addgene #85967 18 nt Perturb-seq barcoded vector, pBA571 Dixit et al., 201626 Addgene #85968 mSWI/SNF KO CRISPR Perturb-seq Library This study N/A lentiCas9-Blast Sanjana et al., 201466 Addgene #52962 psPAX2 plasmid Didier Trono Lab Addgene #12260 pMD2.G plasmid Didier Trono Lab Addgene #11259 (Continued on next page) e1 Molecular Cell 83, 1350–1367.e1–e7, April 20, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Code for analyses in this work (perturbseq_baf version 1.0) This study https://doi.org/10.5281/zenodo.7682087 Cellranger version 3.02 Zheng et al.67 https://support.10xgenomics.com/single- cell-gene-expression/software/pipelines/ latest/installation Scanpy version 1.7.2 Wolf et al.68 https://scanpy.readthedocs.io/en/stable/ MIMOSCA Dixit et al.26 https://github.com/asncd/MIMOSCA Scikit learn version 0.24.1 Pedregosa et al.69 https://scikit-learn.org/stable/index.html Goatools 1.1.6 Klopfenstein et al.70 https://github.com/tanghaibao/goatools SHARE-seq-alignment Ma et al.42 https://github.com/masai1116/SHARE- seq-alignment MACS2 version 2.2.7.1 Zhang et al.71 https://github.com/macs3-project/MACS Seurat version 4.0.4 Hao et al.72 https://satijalab.org/seurat/ Signac version 1.3.0 Stuart et al.73 https://stuartlab.org/signac/ ChromVAR version 1.14.0 Schep et al.74 https://greenleaflab.github.io/chromVAR/ index.html Geosketch version 1.2 Hie et al.75 https://github.com/brianhie/geosketch Other GlutaMAX Supplement Fisher Scientific Cat# 35-050-061 Non-essential Amino Acids Solution (100X) Fisher Scientific Cat# 11-140-050 Sodium Pyruvate (100 mM) Fisher Scientific Cat# 11-360-070 HEPES (1M) Fisher Scientific Cat# 15630080 Penicillin-Streptomycin (10,000 U/mL) Fisher Scientific Cat# 15-140-122 RPMI 1640 Thermo Fisher Scientific Cat# 61870036 DMEM high glucose, no glutamine Thermo Fisher Scientific Cat# 11960044 4%-12% Bis-Tris gels Invitrogen Cat# NP0321 Immobilon PVDF Transfer Membrane Millipore Cat# IPVH00010

Review