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Spatial genomics of AAV vectors reveals mechanism of transcriptional crosstalk that enables targeted delivery of large genetic cargo

Coughlin GM, Borsos M, Barcelona BH, Appling N, Mayfield AMH, Mackey ED, Eser RA, Jackson CR, Chen X, Kumar SR, Gradinaru V
Nat Biotechnol (2025). (Link opens in a new window) Article

Plasmids from Article

ID Plasmid Purpose
231345pAAV.CAG-NLS-EGFP-WPRE-SV40pA-T7-T3-BC(p1-14)Single stranded AAV genome with components for tracking AAV genome via AAV-Zombie. Also expresses a nuclear localized EGFP from CAG promoter.
231346pscAAV.CAG-EGFP-SV40pA-T7-T3-BC(p1-14)Self complementary AAV genome with components for tracking self-complementary AAV genomes via AAV-Zombie. Also expresses EGFP from CAG promoter.
231347pAAV.BC(p1-10)-CAG-EGFP-W3SL-BC(p1-10)Single stranded AAV genome with concatemerization-dependent barcodes, for tracking AAV concatemers via SpECTr. Also expresses EGFP from CAG promoter.
231348pAAV.T7-SP6-BC(p11-14)-CAG-EGFP-W3SL-T7Single stranded AAV genome with barcodeless T7 RNA polymerase promoter and SP6-driven barcode, for tracking AAV concatemers via SpECTr. Also expresses EGFP from CAG promoter.
231349pscAAV.BC(p1-6)-CAG-EGFP-SV40pA-BC(p1-6)Self complementary AAV genome with concatemerization-dependent barcodes, for tracking AAV concatemers via SpECTr. Also expresses EGFP from CAG promoter.
231350pscAAV.T7-SP6-BC(p11-14)-CAG-EGFP-SV40pA-T7Self complementary AAV genome with barcodeless T7 RNA polymerase promoter and SP6-driven barcode, for tracking AAV concatemers via SpECTr. Also expresses EGFP from CAG promoter.
231351pAAV.BC(p1-10)-Ple155-CI-EGFP-W3SL-BC(p1-10)Single stranded AAV genome with concatemerization-dependent barcodes, for tracking AAV concatemers via SpECTr. Also expresses EGFP from Ple155 element, active in Purkinje cells.
231352pAAV.T7-SP6-BC(p11-14)-mDLX-minBG-CI-mRuby2-W3SL-T7Single stranded AAV genome with barcodeless T7 RNA polymerase promoter and SP6-driven barcode, for tracking AAV concatemers via SpECTr. Also expresses mRuby2 from minBG promoter with mDLX enhancer.
231353pAAV.T7-SP6-BC(p11-14)-minBG-CI-mRuby2-W3SL-T7Single stranded AAV genome with barcodeless T7 RNA polymerase promoter and SP6-driven barcode, for tracking AAV concatemers via SpECTr. Also expresses mRuby2 from minBG promoter.
231354pAAV.BC(p1-10)-CMVe-SCP1-TagBFP2-W3SL-BC(p1-10)Single stranded AAV genome with concatemerization-dependent barcodes, for tracking AAV concatemers via SpECTr. Also expresses TagBFP from SCP1 promoter and CMV enhancer.
231355pAAV.BC(p1-10)-SCP1-TagBFP2-W3SL-BC(p1-10)Single stranded AAV genome with concatemerization-dependent barcodes, for tracking AAV concatemers via SpECTr. Also expresses TagBFP from SCP1 promoter.
231356pAAV.T7-SP6-BC(p11-14)-SCP1-tdTomato-W3SL-T7Single stranded AAV genome with barcodeless T7 RNA polymerase promoter and SP6-driven barcode, for tracking AAV concatemers via SpECTr. Also expresses tdTomato from SCP1 promoter.
231357pAAV.T7-SP6-BC(p11-14)-CMVp-CI-mRuby2-W3SL-T7Single stranded AAV genome with barcodeless T7 RNA polymerase promoter and SP6-driven barcode, for tracking AAV concatemers via SpECTr. Also expresses mRuby2 from CMV promoter.
231358pAAV.T7-SP6-BC(p11-14)-Ef1s-CI-mRuby2-W3SL-T7Single stranded AAV genome with barcodeless T7 RNA polymerase promoter and SP6-driven barcode, for tracking AAV concatemers via SpECTr. Also expresses mRuby2 from Ef1s promoter.
231359pAAV.T7-SP6-BC(p11-14)-SCP1-CI-mRuby2-W3SL-T7Single stranded AAV genome with barcodeless T7 RNA polymerase promoter and SP6-driven barcode, for tracking AAV concatemers via SpECTr. Also expresses mRuby2 from SCP1 promoter.
231360pAAV.BC(p1-10)-hDLXI56i-minBG-CI-EGFP-W3SL-BC(p1-10)Single stranded AAV genome with concatemerization-dependent barcodes, for tracking AAV concatemers via SpECTr. Also expresses EGFP from the minBG promoter with hDLXI56i enhancer.
231361pAAV.BC(p1-10)-mscRE4-minBG-CI-EGFP-W3SL-BC(p1-10)Single stranded AAV genome with concatemerization-dependent barcodes, for tracking AAV concatemers via SpECTr. Also expresses EGFP from the minBG promoter with mscRE4 enhancer.
231362pAAV.minBG-EGFP-W3SL_BbsI(GGA)minBG-driven EGFP, containing cassette for BbsI-based Golden Gate assembly (e.g. of sgRNA cassette(s)). Can be used as 'no guide' control.
231363pAAV.Ple155-CI-EGFP-W3SL_BbsI(GGA)Ple155-driven EGFP, containing cassette for BbsI-based Golden Gate assembly (e.g. of sgRNA cassette(s)). Can be used as 'no guide' control.
231364pAAV.Ple155-CI-mRuby2-W3SL_BbsI(GGA)Ple155-driven mRuby2, containing cassette for BbsI-based Golden Gate assembly (e.g. of sgRNA cassette(s)). Can be used as 'no guide' control.
231365pAAV.minBG-EGFP-W3SL_2x-U6-sasgAi14minBG-driven EGFP, also encoding U6-driven sgRNAs to direct saCas9 to both sides of stop cassette in Ai14 mice.
231366pAAV.Ple155-CI-EGFP-W3SL_2x-U6-sasgAi14Ple155-driven EGFP, also encoding U6-driven sgRNAs to direct saCas9 to both sides of stop cassette in Ai14 mice.
231367pAAV.U6-sasgRNA(SapI)_Ple155-CI-EGFP-W3SL_BbsI(GGA)Ple155-driven EGFP, also encoding U6-driven sgRNA cassette, with SapI sites to clone crRNA sequence
231368pAAV.U6-sasgRNA(SapI)_Ple155-CI-mRuby2-W3SL_BbsI(GGA)Ple155-driven mRuby2, also encoding U6-driven sgRNA cassette, with SapI sites to clone crRNA sequence
231369pAAV.minBG-CI-SaCas9-W3SynpAminBG-driven SaCas9, with short synthetic terminator sequence.
231370pAAV.minCMVe-SCP1-SaCas9-W3SynpASCP1 promoter-driven SaCas9 with truncated CMV enhancer and short synthetic terminator sequence.

Antibodies from Article