Recombinant:Article Title: Protocol for CRISPR-Cas9 genome editing of a swine cell line via electroporation.
Article Snippet: Genome editing technology is being used in animals for a variety of purposes, including improvement of animal and public health outcomes.. Characterization of genome editing reagents and anticipated genomic alterations is an essential step toward the development of an edited animal.. Here, we present a protocol for genome editing in the swine testicular (ST) cell line.
Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Purified antibodies conjugated to metal isotopes, see Table S1 Various Various Anti-vimentin rabbit Alexa Fluor-647 conjugate (clone D21H3) Cell Signaling Technology Cat#9856S; RRID:AB_10834530 Anti-Histone 3-176Yb (clone D1H2) Standard BioTools Cat#3176016A; RRID:AB_2847870 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11-965-092 McCoy’s 5A modified medium Gibco Cat#16-600-082 Eagle’s Minimal Essential Medium (EMEM) ATCC Cat#30-2003 Fetal bovine serum (FBS) Hyclone Cat#SH3007-102 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140122 L-Glutamine Gibco Cat#25030081 RPMI-1640 medium Gibco Cat#11875093 Mammary epithelial growth medium (MEGM) Lonza Cat#CC-3051 Geneticin selective antibiotic (G418 sulfate) Gibco Cat#10131035 Dulbecco’s Modified Eagle Medium/Nutrient mixture F-12 (DMEM/F-12) Gibco Cat#11320033 MEM non-essential amino acids (NEAA) Gibco Cat#11140050 Etoposide Sigma-Aldrich Cat#341205 Carboplatin Sigma-Aldrich Cat#2538 Nocodazole Sigma-Aldrich Cat#487928 Talazoparib MedChemExpress Cat#HY-16106 Paclitaxel Sigma-Aldrich Cat#T7402 Rucaparib Selleckchem Cat#S4948 Iododeoxyuridine (IdU) Sigma-Aldrich Cat#I7125 Cisplatin Sigma-Aldrich Cat#P4394 Cell-ID intercalator-103Rh-2000 μM Standard BioTools Cat#201103B 16% Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15711 Antibody stabilization solution Candor Bioscience Cat#131050 Palladium isotopes as nitrate salts Trace Sciences International N/A Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Cell-ID intercalator-Ir Standard BioTools Cat#201192B Calibration Beads, EQ Four Element Standard BioTools Cat#201078 TRIS HCl Sigma-Aldrich Cat#T15760 NaCl Thermo Fisher Cat#S271-3 MgCl2 6H2O Sigma-Aldrich Cat#M2670 Igepal CA-630 Sigma-Aldrich Cat#I8896 DAPI (4’,6-diamidino-2-phenylindole, dihydrochloride) Thermo Fisher Cat#D1306 Critical commercial assays Vybrant® MTT Cell Proliferation Assay Kit Thermo Fisher Cat#V13154 RealTime-GloTM MT Cell Viability Assay Promega Cat#G9711 MaxPAR antibody conjugation kit Standard BioTools N/A (Continued on next page) e1 Cell Reports Medicine 6, 102295, September 16, 2025 Article ll OPEN ACCESS ..
Polymerase Chain Reaction:Article Title: Protocol for CRISPR-Cas9 genome editing of a swine cell line via electroporation.
Article Snippet: Genome editing technology is being used in animals for a variety of purposes, including improvement of animal and public health outcomes.. Characterization of genome editing reagents and anticipated genomic alterations is an essential step toward the development of an edited animal.. Here, we present a protocol for genome editing in the swine testicular (ST) cell line.
Article Title: Phage-assisted evolution and protein engineering yield compact, efficient prime editors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains One Shot Mach1 T1 Phage-Resistant Chemically Competent E. coli Thermo Fisher Scientific Cat#C862003 E. coli S2060 Addgene #105064 Chemicals, peptides, and recombinant proteins BsaI-HFv2 New England BioLabs Cat#R3733S LguI (SapI) Thermo Fisher Scientific Cat#ER1932 T4 DNA Ligase New England BioLabs Cat#M0202S NEBuilder HiFi DNA assembly master mix New England BioLabs Cat#E2621S Dimethyl sulfoxide Sigma-Aldrich Cat#D8418-50ML Poly(ethylene glycol) 3350 Sigma-Aldrich Cat#P4338-500G DNaseI (Rnase-free) New England BioLabs Cat#M0303 Magnesium chloride solution Sigma-Aldrich Cat#M1028-10X1ML Carbenicillin Gold Biotechnology Cat#C-103 Chloramphenicol Gold Biotechnology Cat#C-105 Tetracycline Gold Biotechnology Cat#T-101 Streptomycin Gold Biotechnology Cat#S-150 L-arabinose Gold Biotechnology Cat#A-300 Glucose Sigma-Aldrich Cat#G7021 Bluo-gal Gold Biotechnology Cat#B-673-10 dNTPs New England BioLabs Cat#N0447S Lipofectamine 2000 Thermo Fisher Scientific Cat#11668019 TrypLE Thermo Fisher Scientific Cat#12605010 Proteinase K, recombinant, PCR grade Thermo Fisher Scientific Cat#11668019 SDS (10% wt/vol) Thermo Fisher Scientific Cat#15553027 DNAdvance Kit Beckman Coulter Cat#A48705 AMPure XP Beckman Coulter Cat#B23318 CleanCap Reagent AG TriLink BioTechnologies Cat#N-7113 N1 -Methylpseudouridine50 -Triphosphate TriLink BioTechnologies Cat#N-1081 LiCl Precipitation Solution (7.5 M) Thermo Fisher Scientific Cat#AM9480 DMEM, high glucose, GlutaMAX supplement Thermo Fisher Scientific Cat#10566016 Fetal bovine serum Thermo Fisher Scientific Cat#16000044 L-Glutamine Corning Cat#25-005-Cl Penicillin-Streptomycin Thermo Fisher Scientific Cat#15070063 GlutaMAX supplement Thermo Fisher Scientific Cat#35050061 N-acetyl-L-cysteine Sigma-Aldrich Cat#A7250-100G Human AB Serum Valley Biomedical Cat#HP1022HI Recombinant Human IL-2 Peprotech Cat#200-02 Lymphoprep density gradient medium STEMCELL Technologies Cat#07801 (Continued on next page) Cell 186, 3983–4002.e1–e13, August 31, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Human T-Expander CD3/CD28 Thermo Fisher Scientific Cat#11141D X-VIVO 15 Serum-free Hematopoietic Cell Medium Lonza Cat#BE02-053Q Dulbecco0s Modifi–d Eagle0s Medium – low glucose Sigma-Aldrich Cat#D5546 Eagle’s minimal essential Medium (EMEM) ATCC Cat#30-2003 Opti-MEM reduced serum medium Thermo Fisher Scientific Cat#31985070 PEG 8000 Sigma-Aldrich Cat#25322-68-3 PEG-it Virus Precipitation Solution System Biosciences Cat#LV825A-1 Salt active nuclease ArcticZymes Cat#70910-202 0.9% NaCl Fresenius Kabi Cat#918610 BSA NEB Cat#B9000S Vybrant DyeCycle Ruby Thermo Fisher Cat#V10309 EZ-PREP buffer Sigma-Aldrich #NUC-101 Critical commercial assays Phusion U Multiplex PCR Master Mix Thermo Fisher Scientific Cat#F562L Q5 High-Fidelity 2 x Master Mix New England BioLabs Cat#M0492L Phusion Green Hot Start II High-Fidelity DNA Polymerase Thermo Fisher Scientific Cat#F537L QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 QIAGEN Plasmid Plus Midi Kit QIAGEN Cat#12943 QIAprep Spin Miniprep Kit QIAGEN Cat#27106 Qiagen Plasmid Plus 96 Miniprep Kit QIAGEN Cat#16181 EasySep Human T cell Isolation Kit STEMCELL Technologies Cat#17951 Neon Transfection System Thermo Fisher Scientific Cat#MPK1096 QuickExtract DNA Extraction Solution Lucigen Cat# QE09050 SE Cell Line 4DNucleofector X Kit S Lonza Cat#V4XC-1032 Illustra TempliPhi 100 amplification kit Cytiva Cat#25640010 NEB T7 HiScribe Kit New England BioLabs Cat#E2040S AAVpro Titration Kit version 2 Clontech/Takara Cat#6233 Agencourt DNAdvance Kit Beckman Coulter Cat#V10309 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 MiSeq Reagent Micro Kit v2 (300-cycles) Illumina Cat#MS-103-1002 (Continued on next page) ll OPEN ACCESS e2 Cell 186, 3983–4002.e1–e13, August 31, 2023 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Amplicon sequencing data This paper NCBI SRA: BioProject PRJNA916060 Experimental models: Cell lines Human (female): HEK293T ATCC Cat#CRL-3216 Mouse (male): N2a ATCC Cat#CCL-131 Human (female): HEK293T clone 17 ATCC Cat#CRL-11268 Primary human fibroblast (HEXA) Coriell Institute Cat#GM00221 Primary human fibroblast (UGT1A1) Coriell Institute Cat# GM09551 Primary human fibroblast (RECQL3) Coriell Institute Cat# GM02085 Primary human fibroblast (GAA) Coriell Institute Cat# GM20092 Experimental models: Organisms/strains Timed pregnant C57BL/6J mice Charles River Laboratories Cat#027 Oligonucleotides HEXA, 1278ins TATC pegRNA: mA*mU*mC*rCr UrUrCrCrArGrUrCrArGrGrGrCrCrArUrGrUrUrU rUrArGrArGrCrUrArGrArArArUrArGrCrArArGrUrU rArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCrArCr CrGrArGrUrCrGrGrUrGrCrGrUrArCrCrUrGrArAr CrCrGrUrArUrArUrCrGrUrArUrGrGrCrCrCrUrGr ArCrUrUrCrUrCrUrCrUrCrCrGrCrGrGrUrUrCr UrArUrCrUrArGrUrUrArCrGrCrGrUrUrAr ArArCrCrArArCrUrA*mG*mA*mA Integrated DNA Technologies N/A VEGFA, +2 G to A pegRNA: mG*mA*mU*rGrUr CrUrGrCrArGrGrCrCrArGrArUrGrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGr UrUrArArArArUrArArGrGrCrUrArGrUrCrCr GrUrUrArUrCrArArCrUrUrGrArArArArArGrUrGr GrCrArCrCrGrArGrUrCrGrGrUrGrCrArArUrGrUr GrCrCrArUrCrUrGrGrArGrCrArCrUrCrArUrCrUr GrGrCrCrUrGrCrArGrArArCrArArUrCrUrCrCrGr CrGrGrUrUrCrUrArUrCrUrArGrUrUrArCrGrCr GrUrUrArArArCrCrArArCrUrArGrArA*mU*mU*mU Integrated DNA Technologies N/A DNMT1, 1–15 deletion pegRNA: mG*mA*mU*rUr CrCrUrGrGrUrGrCrCrArGrArArArCrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGrUr UrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCr ArCrCrGrArGrUrCrGrGrUrGrCrArGrGrAr GrGrArArGrCrUrGrCrUrArArGrGrArCrUrArGrUrUr CrUrGrCrCrCrUrUrCrUrGrGrCrArCrCrArGrGrAr CrCrUrCrUrUrCrUrCrGrCrGrGrUrUrCrUrArUr CrUrArGrUrUrArCrGrCrGrUrUrArArArCrCrArArCrUr ArGrArA*mU*mU*mU Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Cell 186, 3983–4002.e1–e13, August 31, 2023 e3 Resource
Next-Generation Sequencing:Article Title: Protocol for CRISPR-Cas9 genome editing of a swine cell line via electroporation.
Article Snippet: Genome editing technology is being used in animals for a variety of purposes, including improvement of animal and public health outcomes.. Characterization of genome editing reagents and anticipated genomic alterations is an essential step toward the development of an edited animal.. Here, we present a protocol for genome editing in the swine testicular (ST) cell line.
Modification:Article Title: Protocol for CRISPR-Cas9 genome editing of a swine cell line via electroporation.
Article Snippet: Genome editing technology is being used in animals for a variety of purposes, including improvement of animal and public health outcomes.. Characterization of genome editing reagents and anticipated genomic alterations is an essential step toward the development of an edited animal.. Here, we present a protocol for genome editing in the swine testicular (ST) cell line.
Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Purified antibodies conjugated to metal isotopes, see Table S1 Various Various Anti-vimentin rabbit Alexa Fluor-647 conjugate (clone D21H3) Cell Signaling Technology Cat#9856S; RRID:AB_10834530 Anti-Histone 3-176Yb (clone D1H2) Standard BioTools Cat#3176016A; RRID:AB_2847870 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11-965-092 McCoy’s 5A modified medium Gibco Cat#16-600-082 Eagle’s Minimal Essential Medium (EMEM) ATCC Cat#30-2003 Fetal bovine serum (FBS) Hyclone Cat#SH3007-102 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140122 L-Glutamine Gibco Cat#25030081 RPMI-1640 medium Gibco Cat#11875093 Mammary epithelial growth medium (MEGM) Lonza Cat#CC-3051 Geneticin selective antibiotic (G418 sulfate) Gibco Cat#10131035 Dulbecco’s Modified Eagle Medium/Nutrient mixture F-12 (DMEM/F-12) Gibco Cat#11320033 MEM non-essential amino acids (NEAA) Gibco Cat#11140050 Etoposide Sigma-Aldrich Cat#341205 Carboplatin Sigma-Aldrich Cat#2538 Nocodazole Sigma-Aldrich Cat#487928 Talazoparib MedChemExpress Cat#HY-16106 Paclitaxel Sigma-Aldrich Cat#T7402 Rucaparib Selleckchem Cat#S4948 Iododeoxyuridine (IdU) Sigma-Aldrich Cat#I7125 Cisplatin Sigma-Aldrich Cat#P4394 Cell-ID intercalator-103Rh-2000 μM Standard BioTools Cat#201103B 16% Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15711 Antibody stabilization solution Candor Bioscience Cat#131050 Palladium isotopes as nitrate salts Trace Sciences International N/A Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Cell-ID intercalator-Ir Standard BioTools Cat#201192B Calibration Beads, EQ Four Element Standard BioTools Cat#201078 TRIS HCl Sigma-Aldrich Cat#T15760 NaCl Thermo Fisher Cat#S271-3 MgCl2 6H2O Sigma-Aldrich Cat#M2670 Igepal CA-630 Sigma-Aldrich Cat#I8896 DAPI (4’,6-diamidino-2-phenylindole, dihydrochloride) Thermo Fisher Cat#D1306 Critical commercial assays Vybrant® MTT Cell Proliferation Assay Kit Thermo Fisher Cat#V13154 RealTime-GloTM MT Cell Viability Assay Promega Cat#G9711 MaxPAR antibody conjugation kit Standard BioTools N/A (Continued on next page) e1 Cell Reports Medicine 6, 102295, September 16, 2025 Article ll OPEN ACCESS ..
Software:Article Title: Protocol for CRISPR-Cas9 genome editing of a swine cell line via electroporation.
Article Snippet: Genome editing technology is being used in animals for a variety of purposes, including improvement of animal and public health outcomes.. Characterization of genome editing reagents and anticipated genomic alterations is an essential step toward the development of an edited animal.. Here, we present a protocol for genome editing in the swine testicular (ST) cell line.
CRISPR:Article Title: Protocol for CRISPR-Cas9 genome editing of a swine cell line via electroporation.
Article Snippet: Genome editing technology is being used in animals for a variety of purposes, including improvement of animal and public health outcomes.. Characterization of genome editing reagents and anticipated genomic alterations is an essential step toward the development of an edited animal.. Here, we present a protocol for genome editing in the swine testicular (ST) cell line.
Purification:Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Purified antibodies conjugated to metal isotopes, see Table S1 Various Various Anti-vimentin rabbit Alexa Fluor-647 conjugate (clone D21H3) Cell Signaling Technology Cat#9856S; RRID:AB_10834530 Anti-Histone 3-176Yb (clone D1H2) Standard BioTools Cat#3176016A; RRID:AB_2847870 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11-965-092 McCoy’s 5A modified medium Gibco Cat#16-600-082 Eagle’s Minimal Essential Medium (EMEM) ATCC Cat#30-2003 Fetal bovine serum (FBS) Hyclone Cat#SH3007-102 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140122 L-Glutamine Gibco Cat#25030081 RPMI-1640 medium Gibco Cat#11875093 Mammary epithelial growth medium (MEGM) Lonza Cat#CC-3051 Geneticin selective antibiotic (G418 sulfate) Gibco Cat#10131035 Dulbecco’s Modified Eagle Medium/Nutrient mixture F-12 (DMEM/F-12) Gibco Cat#11320033 MEM non-essential amino acids (NEAA) Gibco Cat#11140050 Etoposide Sigma-Aldrich Cat#341205 Carboplatin Sigma-Aldrich Cat#2538 Nocodazole Sigma-Aldrich Cat#487928 Talazoparib MedChemExpress Cat#HY-16106 Paclitaxel Sigma-Aldrich Cat#T7402 Rucaparib Selleckchem Cat#S4948 Iododeoxyuridine (IdU) Sigma-Aldrich Cat#I7125 Cisplatin Sigma-Aldrich Cat#P4394 Cell-ID intercalator-103Rh-2000 μM Standard BioTools Cat#201103B 16% Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15711 Antibody stabilization solution Candor Bioscience Cat#131050 Palladium isotopes as nitrate salts Trace Sciences International N/A Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Cell-ID intercalator-Ir Standard BioTools Cat#201192B Calibration Beads, EQ Four Element Standard BioTools Cat#201078 TRIS HCl Sigma-Aldrich Cat#T15760 NaCl Thermo Fisher Cat#S271-3 MgCl2 6H2O Sigma-Aldrich Cat#M2670 Igepal CA-630 Sigma-Aldrich Cat#I8896 DAPI (4’,6-diamidino-2-phenylindole, dihydrochloride) Thermo Fisher Cat#D1306 Critical commercial assays Vybrant® MTT Cell Proliferation Assay Kit Thermo Fisher Cat#V13154 RealTime-GloTM MT Cell Viability Assay Promega Cat#G9711 MaxPAR antibody conjugation kit Standard BioTools N/A (Continued on next page) e1 Cell Reports Medicine 6, 102295, September 16, 2025 Article ll OPEN ACCESS ..
Article Title: Phage-assisted evolution and protein engineering yield compact, efficient prime editors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains One Shot Mach1 T1 Phage-Resistant Chemically Competent E. coli Thermo Fisher Scientific Cat#C862003 E. coli S2060 Addgene #105064 Chemicals, peptides, and recombinant proteins BsaI-HFv2 New England BioLabs Cat#R3733S LguI (SapI) Thermo Fisher Scientific Cat#ER1932 T4 DNA Ligase New England BioLabs Cat#M0202S NEBuilder HiFi DNA assembly master mix New England BioLabs Cat#E2621S Dimethyl sulfoxide Sigma-Aldrich Cat#D8418-50ML Poly(ethylene glycol) 3350 Sigma-Aldrich Cat#P4338-500G DNaseI (Rnase-free) New England BioLabs Cat#M0303 Magnesium chloride solution Sigma-Aldrich Cat#M1028-10X1ML Carbenicillin Gold Biotechnology Cat#C-103 Chloramphenicol Gold Biotechnology Cat#C-105 Tetracycline Gold Biotechnology Cat#T-101 Streptomycin Gold Biotechnology Cat#S-150 L-arabinose Gold Biotechnology Cat#A-300 Glucose Sigma-Aldrich Cat#G7021 Bluo-gal Gold Biotechnology Cat#B-673-10 dNTPs New England BioLabs Cat#N0447S Lipofectamine 2000 Thermo Fisher Scientific Cat#11668019 TrypLE Thermo Fisher Scientific Cat#12605010 Proteinase K, recombinant, PCR grade Thermo Fisher Scientific Cat#11668019 SDS (10% wt/vol) Thermo Fisher Scientific Cat#15553027 DNAdvance Kit Beckman Coulter Cat#A48705 AMPure XP Beckman Coulter Cat#B23318 CleanCap Reagent AG TriLink BioTechnologies Cat#N-7113 N1 -Methylpseudouridine50 -Triphosphate TriLink BioTechnologies Cat#N-1081 LiCl Precipitation Solution (7.5 M) Thermo Fisher Scientific Cat#AM9480 DMEM, high glucose, GlutaMAX supplement Thermo Fisher Scientific Cat#10566016 Fetal bovine serum Thermo Fisher Scientific Cat#16000044 L-Glutamine Corning Cat#25-005-Cl Penicillin-Streptomycin Thermo Fisher Scientific Cat#15070063 GlutaMAX supplement Thermo Fisher Scientific Cat#35050061 N-acetyl-L-cysteine Sigma-Aldrich Cat#A7250-100G Human AB Serum Valley Biomedical Cat#HP1022HI Recombinant Human IL-2 Peprotech Cat#200-02 Lymphoprep density gradient medium STEMCELL Technologies Cat#07801 (Continued on next page) Cell 186, 3983–4002.e1–e13, August 31, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Human T-Expander CD3/CD28 Thermo Fisher Scientific Cat#11141D X-VIVO 15 Serum-free Hematopoietic Cell Medium Lonza Cat#BE02-053Q Dulbecco0s Modifi–d Eagle0s Medium – low glucose Sigma-Aldrich Cat#D5546 Eagle’s minimal essential Medium (EMEM) ATCC Cat#30-2003 Opti-MEM reduced serum medium Thermo Fisher Scientific Cat#31985070 PEG 8000 Sigma-Aldrich Cat#25322-68-3 PEG-it Virus Precipitation Solution System Biosciences Cat#LV825A-1 Salt active nuclease ArcticZymes Cat#70910-202 0.9% NaCl Fresenius Kabi Cat#918610 BSA NEB Cat#B9000S Vybrant DyeCycle Ruby Thermo Fisher Cat#V10309 EZ-PREP buffer Sigma-Aldrich #NUC-101 Critical commercial assays Phusion U Multiplex PCR Master Mix Thermo Fisher Scientific Cat#F562L Q5 High-Fidelity 2 x Master Mix New England BioLabs Cat#M0492L Phusion Green Hot Start II High-Fidelity DNA Polymerase Thermo Fisher Scientific Cat#F537L QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 QIAGEN Plasmid Plus Midi Kit QIAGEN Cat#12943 QIAprep Spin Miniprep Kit QIAGEN Cat#27106 Qiagen Plasmid Plus 96 Miniprep Kit QIAGEN Cat#16181 EasySep Human T cell Isolation Kit STEMCELL Technologies Cat#17951 Neon Transfection System Thermo Fisher Scientific Cat#MPK1096 QuickExtract DNA Extraction Solution Lucigen Cat# QE09050 SE Cell Line 4DNucleofector X Kit S Lonza Cat#V4XC-1032 Illustra TempliPhi 100 amplification kit Cytiva Cat#25640010 NEB T7 HiScribe Kit New England BioLabs Cat#E2040S AAVpro Titration Kit version 2 Clontech/Takara Cat#6233 Agencourt DNAdvance Kit Beckman Coulter Cat#V10309 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 MiSeq Reagent Micro Kit v2 (300-cycles) Illumina Cat#MS-103-1002 (Continued on next page) ll OPEN ACCESS e2 Cell 186, 3983–4002.e1–e13, August 31, 2023 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Amplicon sequencing data This paper NCBI SRA: BioProject PRJNA916060 Experimental models: Cell lines Human (female): HEK293T ATCC Cat#CRL-3216 Mouse (male): N2a ATCC Cat#CCL-131 Human (female): HEK293T clone 17 ATCC Cat#CRL-11268 Primary human fibroblast (HEXA) Coriell Institute Cat#GM00221 Primary human fibroblast (UGT1A1) Coriell Institute Cat# GM09551 Primary human fibroblast (RECQL3) Coriell Institute Cat# GM02085 Primary human fibroblast (GAA) Coriell Institute Cat# GM20092 Experimental models: Organisms/strains Timed pregnant C57BL/6J mice Charles River Laboratories Cat#027 Oligonucleotides HEXA, 1278ins TATC pegRNA: mA*mU*mC*rCr UrUrCrCrArGrUrCrArGrGrGrCrCrArUrGrUrUrU rUrArGrArGrCrUrArGrArArArUrArGrCrArArGrUrU rArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCrArCr CrGrArGrUrCrGrGrUrGrCrGrUrArCrCrUrGrArAr CrCrGrUrArUrArUrCrGrUrArUrGrGrCrCrCrUrGr ArCrUrUrCrUrCrUrCrUrCrCrGrCrGrGrUrUrCr UrArUrCrUrArGrUrUrArCrGrCrGrUrUrAr ArArCrCrArArCrUrA*mG*mA*mA Integrated DNA Technologies N/A VEGFA, +2 G to A pegRNA: mG*mA*mU*rGrUr CrUrGrCrArGrGrCrCrArGrArUrGrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGr UrUrArArArArUrArArGrGrCrUrArGrUrCrCr GrUrUrArUrCrArArCrUrUrGrArArArArArGrUrGr GrCrArCrCrGrArGrUrCrGrGrUrGrCrArArUrGrUr GrCrCrArUrCrUrGrGrArGrCrArCrUrCrArUrCrUr GrGrCrCrUrGrCrArGrArArCrArArUrCrUrCrCrGr CrGrGrUrUrCrUrArUrCrUrArGrUrUrArCrGrCr GrUrUrArArArCrCrArArCrUrArGrArA*mU*mU*mU Integrated DNA Technologies N/A DNMT1, 1–15 deletion pegRNA: mG*mA*mU*rUr CrCrUrGrGrUrGrCrCrArGrArArArCrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGrUr UrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCr ArCrCrGrArGrUrCrGrGrUrGrCrArGrGrAr GrGrArArGrCrUrGrCrUrArArGrGrArCrUrArGrUrUr CrUrGrCrCrCrUrUrCrUrGrGrCrArCrCrArGrGrAr CrCrUrCrUrUrCrUrCrGrCrGrGrUrUrCrUrArUr CrUrArGrUrUrArCrGrCrGrUrUrArArArCrCrArArCrUr ArGrArA*mU*mU*mU Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Cell 186, 3983–4002.e1–e13, August 31, 2023 e3 Resource
Electron Microscopy:Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Purified antibodies conjugated to metal isotopes, see Table S1 Various Various Anti-vimentin rabbit Alexa Fluor-647 conjugate (clone D21H3) Cell Signaling Technology Cat#9856S; RRID:AB_10834530 Anti-Histone 3-176Yb (clone D1H2) Standard BioTools Cat#3176016A; RRID:AB_2847870 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11-965-092 McCoy’s 5A modified medium Gibco Cat#16-600-082 Eagle’s Minimal Essential Medium (EMEM) ATCC Cat#30-2003 Fetal bovine serum (FBS) Hyclone Cat#SH3007-102 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140122 L-Glutamine Gibco Cat#25030081 RPMI-1640 medium Gibco Cat#11875093 Mammary epithelial growth medium (MEGM) Lonza Cat#CC-3051 Geneticin selective antibiotic (G418 sulfate) Gibco Cat#10131035 Dulbecco’s Modified Eagle Medium/Nutrient mixture F-12 (DMEM/F-12) Gibco Cat#11320033 MEM non-essential amino acids (NEAA) Gibco Cat#11140050 Etoposide Sigma-Aldrich Cat#341205 Carboplatin Sigma-Aldrich Cat#2538 Nocodazole Sigma-Aldrich Cat#487928 Talazoparib MedChemExpress Cat#HY-16106 Paclitaxel Sigma-Aldrich Cat#T7402 Rucaparib Selleckchem Cat#S4948 Iododeoxyuridine (IdU) Sigma-Aldrich Cat#I7125 Cisplatin Sigma-Aldrich Cat#P4394 Cell-ID intercalator-103Rh-2000 μM Standard BioTools Cat#201103B 16% Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15711 Antibody stabilization solution Candor Bioscience Cat#131050 Palladium isotopes as nitrate salts Trace Sciences International N/A Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Cell-ID intercalator-Ir Standard BioTools Cat#201192B Calibration Beads, EQ Four Element Standard BioTools Cat#201078 TRIS HCl Sigma-Aldrich Cat#T15760 NaCl Thermo Fisher Cat#S271-3 MgCl2 6H2O Sigma-Aldrich Cat#M2670 Igepal CA-630 Sigma-Aldrich Cat#I8896 DAPI (4’,6-diamidino-2-phenylindole, dihydrochloride) Thermo Fisher Cat#D1306 Critical commercial assays Vybrant® MTT Cell Proliferation Assay Kit Thermo Fisher Cat#V13154 RealTime-GloTM MT Cell Viability Assay Promega Cat#G9711 MaxPAR antibody conjugation kit Standard BioTools N/A (Continued on next page) e1 Cell Reports Medicine 6, 102295, September 16, 2025 Article ll OPEN ACCESS ..
Blocking Assay:Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Purified antibodies conjugated to metal isotopes, see Table S1 Various Various Anti-vimentin rabbit Alexa Fluor-647 conjugate (clone D21H3) Cell Signaling Technology Cat#9856S; RRID:AB_10834530 Anti-Histone 3-176Yb (clone D1H2) Standard BioTools Cat#3176016A; RRID:AB_2847870 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11-965-092 McCoy’s 5A modified medium Gibco Cat#16-600-082 Eagle’s Minimal Essential Medium (EMEM) ATCC Cat#30-2003 Fetal bovine serum (FBS) Hyclone Cat#SH3007-102 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140122 L-Glutamine Gibco Cat#25030081 RPMI-1640 medium Gibco Cat#11875093 Mammary epithelial growth medium (MEGM) Lonza Cat#CC-3051 Geneticin selective antibiotic (G418 sulfate) Gibco Cat#10131035 Dulbecco’s Modified Eagle Medium/Nutrient mixture F-12 (DMEM/F-12) Gibco Cat#11320033 MEM non-essential amino acids (NEAA) Gibco Cat#11140050 Etoposide Sigma-Aldrich Cat#341205 Carboplatin Sigma-Aldrich Cat#2538 Nocodazole Sigma-Aldrich Cat#487928 Talazoparib MedChemExpress Cat#HY-16106 Paclitaxel Sigma-Aldrich Cat#T7402 Rucaparib Selleckchem Cat#S4948 Iododeoxyuridine (IdU) Sigma-Aldrich Cat#I7125 Cisplatin Sigma-Aldrich Cat#P4394 Cell-ID intercalator-103Rh-2000 μM Standard BioTools Cat#201103B 16% Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15711 Antibody stabilization solution Candor Bioscience Cat#131050 Palladium isotopes as nitrate salts Trace Sciences International N/A Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Cell-ID intercalator-Ir Standard BioTools Cat#201192B Calibration Beads, EQ Four Element Standard BioTools Cat#201078 TRIS HCl Sigma-Aldrich Cat#T15760 NaCl Thermo Fisher Cat#S271-3 MgCl2 6H2O Sigma-Aldrich Cat#M2670 Igepal CA-630 Sigma-Aldrich Cat#I8896 DAPI (4’,6-diamidino-2-phenylindole, dihydrochloride) Thermo Fisher Cat#D1306 Critical commercial assays Vybrant® MTT Cell Proliferation Assay Kit Thermo Fisher Cat#V13154 RealTime-GloTM MT Cell Viability Assay Promega Cat#G9711 MaxPAR antibody conjugation kit Standard BioTools N/A (Continued on next page) e1 Cell Reports Medicine 6, 102295, September 16, 2025 Article ll OPEN ACCESS ..
MTT Assay:Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Purified antibodies conjugated to metal isotopes, see Table S1 Various Various Anti-vimentin rabbit Alexa Fluor-647 conjugate (clone D21H3) Cell Signaling Technology Cat#9856S; RRID:AB_10834530 Anti-Histone 3-176Yb (clone D1H2) Standard BioTools Cat#3176016A; RRID:AB_2847870 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11-965-092 McCoy’s 5A modified medium Gibco Cat#16-600-082 Eagle’s Minimal Essential Medium (EMEM) ATCC Cat#30-2003 Fetal bovine serum (FBS) Hyclone Cat#SH3007-102 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140122 L-Glutamine Gibco Cat#25030081 RPMI-1640 medium Gibco Cat#11875093 Mammary epithelial growth medium (MEGM) Lonza Cat#CC-3051 Geneticin selective antibiotic (G418 sulfate) Gibco Cat#10131035 Dulbecco’s Modified Eagle Medium/Nutrient mixture F-12 (DMEM/F-12) Gibco Cat#11320033 MEM non-essential amino acids (NEAA) Gibco Cat#11140050 Etoposide Sigma-Aldrich Cat#341205 Carboplatin Sigma-Aldrich Cat#2538 Nocodazole Sigma-Aldrich Cat#487928 Talazoparib MedChemExpress Cat#HY-16106 Paclitaxel Sigma-Aldrich Cat#T7402 Rucaparib Selleckchem Cat#S4948 Iododeoxyuridine (IdU) Sigma-Aldrich Cat#I7125 Cisplatin Sigma-Aldrich Cat#P4394 Cell-ID intercalator-103Rh-2000 μM Standard BioTools Cat#201103B 16% Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15711 Antibody stabilization solution Candor Bioscience Cat#131050 Palladium isotopes as nitrate salts Trace Sciences International N/A Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Cell-ID intercalator-Ir Standard BioTools Cat#201192B Calibration Beads, EQ Four Element Standard BioTools Cat#201078 TRIS HCl Sigma-Aldrich Cat#T15760 NaCl Thermo Fisher Cat#S271-3 MgCl2 6H2O Sigma-Aldrich Cat#M2670 Igepal CA-630 Sigma-Aldrich Cat#I8896 DAPI (4’,6-diamidino-2-phenylindole, dihydrochloride) Thermo Fisher Cat#D1306 Critical commercial assays Vybrant® MTT Cell Proliferation Assay Kit Thermo Fisher Cat#V13154 RealTime-GloTM MT Cell Viability Assay Promega Cat#G9711 MaxPAR antibody conjugation kit Standard BioTools N/A (Continued on next page) e1 Cell Reports Medicine 6, 102295, September 16, 2025 Article ll OPEN ACCESS ..
Proliferation Assay:Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Purified antibodies conjugated to metal isotopes, see Table S1 Various Various Anti-vimentin rabbit Alexa Fluor-647 conjugate (clone D21H3) Cell Signaling Technology Cat#9856S; RRID:AB_10834530 Anti-Histone 3-176Yb (clone D1H2) Standard BioTools Cat#3176016A; RRID:AB_2847870 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11-965-092 McCoy’s 5A modified medium Gibco Cat#16-600-082 Eagle’s Minimal Essential Medium (EMEM) ATCC Cat#30-2003 Fetal bovine serum (FBS) Hyclone Cat#SH3007-102 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140122 L-Glutamine Gibco Cat#25030081 RPMI-1640 medium Gibco Cat#11875093 Mammary epithelial growth medium (MEGM) Lonza Cat#CC-3051 Geneticin selective antibiotic (G418 sulfate) Gibco Cat#10131035 Dulbecco’s Modified Eagle Medium/Nutrient mixture F-12 (DMEM/F-12) Gibco Cat#11320033 MEM non-essential amino acids (NEAA) Gibco Cat#11140050 Etoposide Sigma-Aldrich Cat#341205 Carboplatin Sigma-Aldrich Cat#2538 Nocodazole Sigma-Aldrich Cat#487928 Talazoparib MedChemExpress Cat#HY-16106 Paclitaxel Sigma-Aldrich Cat#T7402 Rucaparib Selleckchem Cat#S4948 Iododeoxyuridine (IdU) Sigma-Aldrich Cat#I7125 Cisplatin Sigma-Aldrich Cat#P4394 Cell-ID intercalator-103Rh-2000 μM Standard BioTools Cat#201103B 16% Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15711 Antibody stabilization solution Candor Bioscience Cat#131050 Palladium isotopes as nitrate salts Trace Sciences International N/A Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Cell-ID intercalator-Ir Standard BioTools Cat#201192B Calibration Beads, EQ Four Element Standard BioTools Cat#201078 TRIS HCl Sigma-Aldrich Cat#T15760 NaCl Thermo Fisher Cat#S271-3 MgCl2 6H2O Sigma-Aldrich Cat#M2670 Igepal CA-630 Sigma-Aldrich Cat#I8896 DAPI (4’,6-diamidino-2-phenylindole, dihydrochloride) Thermo Fisher Cat#D1306 Critical commercial assays Vybrant® MTT Cell Proliferation Assay Kit Thermo Fisher Cat#V13154 RealTime-GloTM MT Cell Viability Assay Promega Cat#G9711 MaxPAR antibody conjugation kit Standard BioTools N/A (Continued on next page) e1 Cell Reports Medicine 6, 102295, September 16, 2025 Article ll OPEN ACCESS ..
Viability Assay:Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Purified antibodies conjugated to metal isotopes, see Table S1 Various Various Anti-vimentin rabbit Alexa Fluor-647 conjugate (clone D21H3) Cell Signaling Technology Cat#9856S; RRID:AB_10834530 Anti-Histone 3-176Yb (clone D1H2) Standard BioTools Cat#3176016A; RRID:AB_2847870 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11-965-092 McCoy’s 5A modified medium Gibco Cat#16-600-082 Eagle’s Minimal Essential Medium (EMEM) ATCC Cat#30-2003 Fetal bovine serum (FBS) Hyclone Cat#SH3007-102 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140122 L-Glutamine Gibco Cat#25030081 RPMI-1640 medium Gibco Cat#11875093 Mammary epithelial growth medium (MEGM) Lonza Cat#CC-3051 Geneticin selective antibiotic (G418 sulfate) Gibco Cat#10131035 Dulbecco’s Modified Eagle Medium/Nutrient mixture F-12 (DMEM/F-12) Gibco Cat#11320033 MEM non-essential amino acids (NEAA) Gibco Cat#11140050 Etoposide Sigma-Aldrich Cat#341205 Carboplatin Sigma-Aldrich Cat#2538 Nocodazole Sigma-Aldrich Cat#487928 Talazoparib MedChemExpress Cat#HY-16106 Paclitaxel Sigma-Aldrich Cat#T7402 Rucaparib Selleckchem Cat#S4948 Iododeoxyuridine (IdU) Sigma-Aldrich Cat#I7125 Cisplatin Sigma-Aldrich Cat#P4394 Cell-ID intercalator-103Rh-2000 μM Standard BioTools Cat#201103B 16% Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15711 Antibody stabilization solution Candor Bioscience Cat#131050 Palladium isotopes as nitrate salts Trace Sciences International N/A Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Cell-ID intercalator-Ir Standard BioTools Cat#201192B Calibration Beads, EQ Four Element Standard BioTools Cat#201078 TRIS HCl Sigma-Aldrich Cat#T15760 NaCl Thermo Fisher Cat#S271-3 MgCl2 6H2O Sigma-Aldrich Cat#M2670 Igepal CA-630 Sigma-Aldrich Cat#I8896 DAPI (4’,6-diamidino-2-phenylindole, dihydrochloride) Thermo Fisher Cat#D1306 Critical commercial assays Vybrant® MTT Cell Proliferation Assay Kit Thermo Fisher Cat#V13154 RealTime-GloTM MT Cell Viability Assay Promega Cat#G9711 MaxPAR antibody conjugation kit Standard BioTools N/A (Continued on next page) e1 Cell Reports Medicine 6, 102295, September 16, 2025 Article ll OPEN ACCESS ..
Conjugation Assay:Article Title: Coordinated protein modules define DNA damage responses to carboplatin at single-cell resolution in human ovarian carcinoma models
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Purified antibodies conjugated to metal isotopes, see Table S1 Various Various Anti-vimentin rabbit Alexa Fluor-647 conjugate (clone D21H3) Cell Signaling Technology Cat#9856S; RRID:AB_10834530 Anti-Histone 3-176Yb (clone D1H2) Standard BioTools Cat#3176016A; RRID:AB_2847870 Chemicals, peptides, and recombinant proteins Dulbecco’s Modified Eagle Medium (DMEM) Gibco Cat#11-965-092 McCoy’s 5A modified medium Gibco Cat#16-600-082 Eagle’s Minimal Essential Medium (EMEM) ATCC Cat#30-2003 Fetal bovine serum (FBS) Hyclone Cat#SH3007-102 Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140122 L-Glutamine Gibco Cat#25030081 RPMI-1640 medium Gibco Cat#11875093 Mammary epithelial growth medium (MEGM) Lonza Cat#CC-3051 Geneticin selective antibiotic (G418 sulfate) Gibco Cat#10131035 Dulbecco’s Modified Eagle Medium/Nutrient mixture F-12 (DMEM/F-12) Gibco Cat#11320033 MEM non-essential amino acids (NEAA) Gibco Cat#11140050 Etoposide Sigma-Aldrich Cat#341205 Carboplatin Sigma-Aldrich Cat#2538 Nocodazole Sigma-Aldrich Cat#487928 Talazoparib MedChemExpress Cat#HY-16106 Paclitaxel Sigma-Aldrich Cat#T7402 Rucaparib Selleckchem Cat#S4948 Iododeoxyuridine (IdU) Sigma-Aldrich Cat#I7125 Cisplatin Sigma-Aldrich Cat#P4394 Cell-ID intercalator-103Rh-2000 μM Standard BioTools Cat#201103B 16% Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15711 Antibody stabilization solution Candor Bioscience Cat#131050 Palladium isotopes as nitrate salts Trace Sciences International N/A Human TruStain FcX (Fc Receptor Blocking Solution) BioLegend Cat#422302 Cell-ID intercalator-Ir Standard BioTools Cat#201192B Calibration Beads, EQ Four Element Standard BioTools Cat#201078 TRIS HCl Sigma-Aldrich Cat#T15760 NaCl Thermo Fisher Cat#S271-3 MgCl2 6H2O Sigma-Aldrich Cat#M2670 Igepal CA-630 Sigma-Aldrich Cat#I8896 DAPI (4’,6-diamidino-2-phenylindole, dihydrochloride) Thermo Fisher Cat#D1306 Critical commercial assays Vybrant® MTT Cell Proliferation Assay Kit Thermo Fisher Cat#V13154 RealTime-GloTM MT Cell Viability Assay Promega Cat#G9711 MaxPAR antibody conjugation kit Standard BioTools N/A (Continued on next page) e1 Cell Reports Medicine 6, 102295, September 16, 2025 Article ll OPEN ACCESS ..
Virus:Article Title: Phage-assisted evolution and protein engineering yield compact, efficient prime editors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains One Shot Mach1 T1 Phage-Resistant Chemically Competent E. coli Thermo Fisher Scientific Cat#C862003 E. coli S2060 Addgene #105064 Chemicals, peptides, and recombinant proteins BsaI-HFv2 New England BioLabs Cat#R3733S LguI (SapI) Thermo Fisher Scientific Cat#ER1932 T4 DNA Ligase New England BioLabs Cat#M0202S NEBuilder HiFi DNA assembly master mix New England BioLabs Cat#E2621S Dimethyl sulfoxide Sigma-Aldrich Cat#D8418-50ML Poly(ethylene glycol) 3350 Sigma-Aldrich Cat#P4338-500G DNaseI (Rnase-free) New England BioLabs Cat#M0303 Magnesium chloride solution Sigma-Aldrich Cat#M1028-10X1ML Carbenicillin Gold Biotechnology Cat#C-103 Chloramphenicol Gold Biotechnology Cat#C-105 Tetracycline Gold Biotechnology Cat#T-101 Streptomycin Gold Biotechnology Cat#S-150 L-arabinose Gold Biotechnology Cat#A-300 Glucose Sigma-Aldrich Cat#G7021 Bluo-gal Gold Biotechnology Cat#B-673-10 dNTPs New England BioLabs Cat#N0447S Lipofectamine 2000 Thermo Fisher Scientific Cat#11668019 TrypLE Thermo Fisher Scientific Cat#12605010 Proteinase K, recombinant, PCR grade Thermo Fisher Scientific Cat#11668019 SDS (10% wt/vol) Thermo Fisher Scientific Cat#15553027 DNAdvance Kit Beckman Coulter Cat#A48705 AMPure XP Beckman Coulter Cat#B23318 CleanCap Reagent AG TriLink BioTechnologies Cat#N-7113 N1 -Methylpseudouridine50 -Triphosphate TriLink BioTechnologies Cat#N-1081 LiCl Precipitation Solution (7.5 M) Thermo Fisher Scientific Cat#AM9480 DMEM, high glucose, GlutaMAX supplement Thermo Fisher Scientific Cat#10566016 Fetal bovine serum Thermo Fisher Scientific Cat#16000044 L-Glutamine Corning Cat#25-005-Cl Penicillin-Streptomycin Thermo Fisher Scientific Cat#15070063 GlutaMAX supplement Thermo Fisher Scientific Cat#35050061 N-acetyl-L-cysteine Sigma-Aldrich Cat#A7250-100G Human AB Serum Valley Biomedical Cat#HP1022HI Recombinant Human IL-2 Peprotech Cat#200-02 Lymphoprep density gradient medium STEMCELL Technologies Cat#07801 (Continued on next page) Cell 186, 3983–4002.e1–e13, August 31, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Human T-Expander CD3/CD28 Thermo Fisher Scientific Cat#11141D X-VIVO 15 Serum-free Hematopoietic Cell Medium Lonza Cat#BE02-053Q Dulbecco0s Modifi–d Eagle0s Medium – low glucose Sigma-Aldrich Cat#D5546 Eagle’s minimal essential Medium (EMEM) ATCC Cat#30-2003 Opti-MEM reduced serum medium Thermo Fisher Scientific Cat#31985070 PEG 8000 Sigma-Aldrich Cat#25322-68-3 PEG-it Virus Precipitation Solution System Biosciences Cat#LV825A-1 Salt active nuclease ArcticZymes Cat#70910-202 0.9% NaCl Fresenius Kabi Cat#918610 BSA NEB Cat#B9000S Vybrant DyeCycle Ruby Thermo Fisher Cat#V10309 EZ-PREP buffer Sigma-Aldrich #NUC-101 Critical commercial assays Phusion U Multiplex PCR Master Mix Thermo Fisher Scientific Cat#F562L Q5 High-Fidelity 2 x Master Mix New England BioLabs Cat#M0492L Phusion Green Hot Start II High-Fidelity DNA Polymerase Thermo Fisher Scientific Cat#F537L QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 QIAGEN Plasmid Plus Midi Kit QIAGEN Cat#12943 QIAprep Spin Miniprep Kit QIAGEN Cat#27106 Qiagen Plasmid Plus 96 Miniprep Kit QIAGEN Cat#16181 EasySep Human T cell Isolation Kit STEMCELL Technologies Cat#17951 Neon Transfection System Thermo Fisher Scientific Cat#MPK1096 QuickExtract DNA Extraction Solution Lucigen Cat# QE09050 SE Cell Line 4DNucleofector X Kit S Lonza Cat#V4XC-1032 Illustra TempliPhi 100 amplification kit Cytiva Cat#25640010 NEB T7 HiScribe Kit New England BioLabs Cat#E2040S AAVpro Titration Kit version 2 Clontech/Takara Cat#6233 Agencourt DNAdvance Kit Beckman Coulter Cat#V10309 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 MiSeq Reagent Micro Kit v2 (300-cycles) Illumina Cat#MS-103-1002 (Continued on next page) ll OPEN ACCESS e2 Cell 186, 3983–4002.e1–e13, August 31, 2023 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Amplicon sequencing data This paper NCBI SRA: BioProject PRJNA916060 Experimental models: Cell lines Human (female): HEK293T ATCC Cat#CRL-3216 Mouse (male): N2a ATCC Cat#CCL-131 Human (female): HEK293T clone 17 ATCC Cat#CRL-11268 Primary human fibroblast (HEXA) Coriell Institute Cat#GM00221 Primary human fibroblast (UGT1A1) Coriell Institute Cat# GM09551 Primary human fibroblast (RECQL3) Coriell Institute Cat# GM02085 Primary human fibroblast (GAA) Coriell Institute Cat# GM20092 Experimental models: Organisms/strains Timed pregnant C57BL/6J mice Charles River Laboratories Cat#027 Oligonucleotides HEXA, 1278ins TATC pegRNA: mA*mU*mC*rCr UrUrCrCrArGrUrCrArGrGrGrCrCrArUrGrUrUrU rUrArGrArGrCrUrArGrArArArUrArGrCrArArGrUrU rArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCrArCr CrGrArGrUrCrGrGrUrGrCrGrUrArCrCrUrGrArAr CrCrGrUrArUrArUrCrGrUrArUrGrGrCrCrCrUrGr ArCrUrUrCrUrCrUrCrUrCrCrGrCrGrGrUrUrCr UrArUrCrUrArGrUrUrArCrGrCrGrUrUrAr ArArCrCrArArCrUrA*mG*mA*mA Integrated DNA Technologies N/A VEGFA, +2 G to A pegRNA: mG*mA*mU*rGrUr CrUrGrCrArGrGrCrCrArGrArUrGrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGr UrUrArArArArUrArArGrGrCrUrArGrUrCrCr GrUrUrArUrCrArArCrUrUrGrArArArArArGrUrGr GrCrArCrCrGrArGrUrCrGrGrUrGrCrArArUrGrUr GrCrCrArUrCrUrGrGrArGrCrArCrUrCrArUrCrUr GrGrCrCrUrGrCrArGrArArCrArArUrCrUrCrCrGr CrGrGrUrUrCrUrArUrCrUrArGrUrUrArCrGrCr GrUrUrArArArCrCrArArCrUrArGrArA*mU*mU*mU Integrated DNA Technologies N/A DNMT1, 1–15 deletion pegRNA: mG*mA*mU*rUr CrCrUrGrGrUrGrCrCrArGrArArArCrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGrUr UrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCr ArCrCrGrArGrUrCrGrGrUrGrCrArGrGrAr GrGrArArGrCrUrGrCrUrArArGrGrArCrUrArGrUrUr CrUrGrCrCrCrUrUrCrUrGrGrCrArCrCrArGrGrAr CrCrUrCrUrUrCrUrCrGrCrGrGrUrUrCrUrArUr CrUrArGrUrUrArCrGrCrGrUrUrArArArCrCrArArCrUr ArGrArA*mU*mU*mU Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Cell 186, 3983–4002.e1–e13, August 31, 2023 e3 Resource
Multiplex Assay:Article Title: Phage-assisted evolution and protein engineering yield compact, efficient prime editors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains One Shot Mach1 T1 Phage-Resistant Chemically Competent E. coli Thermo Fisher Scientific Cat#C862003 E. coli S2060 Addgene #105064 Chemicals, peptides, and recombinant proteins BsaI-HFv2 New England BioLabs Cat#R3733S LguI (SapI) Thermo Fisher Scientific Cat#ER1932 T4 DNA Ligase New England BioLabs Cat#M0202S NEBuilder HiFi DNA assembly master mix New England BioLabs Cat#E2621S Dimethyl sulfoxide Sigma-Aldrich Cat#D8418-50ML Poly(ethylene glycol) 3350 Sigma-Aldrich Cat#P4338-500G DNaseI (Rnase-free) New England BioLabs Cat#M0303 Magnesium chloride solution Sigma-Aldrich Cat#M1028-10X1ML Carbenicillin Gold Biotechnology Cat#C-103 Chloramphenicol Gold Biotechnology Cat#C-105 Tetracycline Gold Biotechnology Cat#T-101 Streptomycin Gold Biotechnology Cat#S-150 L-arabinose Gold Biotechnology Cat#A-300 Glucose Sigma-Aldrich Cat#G7021 Bluo-gal Gold Biotechnology Cat#B-673-10 dNTPs New England BioLabs Cat#N0447S Lipofectamine 2000 Thermo Fisher Scientific Cat#11668019 TrypLE Thermo Fisher Scientific Cat#12605010 Proteinase K, recombinant, PCR grade Thermo Fisher Scientific Cat#11668019 SDS (10% wt/vol) Thermo Fisher Scientific Cat#15553027 DNAdvance Kit Beckman Coulter Cat#A48705 AMPure XP Beckman Coulter Cat#B23318 CleanCap Reagent AG TriLink BioTechnologies Cat#N-7113 N1 -Methylpseudouridine50 -Triphosphate TriLink BioTechnologies Cat#N-1081 LiCl Precipitation Solution (7.5 M) Thermo Fisher Scientific Cat#AM9480 DMEM, high glucose, GlutaMAX supplement Thermo Fisher Scientific Cat#10566016 Fetal bovine serum Thermo Fisher Scientific Cat#16000044 L-Glutamine Corning Cat#25-005-Cl Penicillin-Streptomycin Thermo Fisher Scientific Cat#15070063 GlutaMAX supplement Thermo Fisher Scientific Cat#35050061 N-acetyl-L-cysteine Sigma-Aldrich Cat#A7250-100G Human AB Serum Valley Biomedical Cat#HP1022HI Recombinant Human IL-2 Peprotech Cat#200-02 Lymphoprep density gradient medium STEMCELL Technologies Cat#07801 (Continued on next page) Cell 186, 3983–4002.e1–e13, August 31, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Human T-Expander CD3/CD28 Thermo Fisher Scientific Cat#11141D X-VIVO 15 Serum-free Hematopoietic Cell Medium Lonza Cat#BE02-053Q Dulbecco0s Modifi–d Eagle0s Medium – low glucose Sigma-Aldrich Cat#D5546 Eagle’s minimal essential Medium (EMEM) ATCC Cat#30-2003 Opti-MEM reduced serum medium Thermo Fisher Scientific Cat#31985070 PEG 8000 Sigma-Aldrich Cat#25322-68-3 PEG-it Virus Precipitation Solution System Biosciences Cat#LV825A-1 Salt active nuclease ArcticZymes Cat#70910-202 0.9% NaCl Fresenius Kabi Cat#918610 BSA NEB Cat#B9000S Vybrant DyeCycle Ruby Thermo Fisher Cat#V10309 EZ-PREP buffer Sigma-Aldrich #NUC-101 Critical commercial assays Phusion U Multiplex PCR Master Mix Thermo Fisher Scientific Cat#F562L Q5 High-Fidelity 2 x Master Mix New England BioLabs Cat#M0492L Phusion Green Hot Start II High-Fidelity DNA Polymerase Thermo Fisher Scientific Cat#F537L QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 QIAGEN Plasmid Plus Midi Kit QIAGEN Cat#12943 QIAprep Spin Miniprep Kit QIAGEN Cat#27106 Qiagen Plasmid Plus 96 Miniprep Kit QIAGEN Cat#16181 EasySep Human T cell Isolation Kit STEMCELL Technologies Cat#17951 Neon Transfection System Thermo Fisher Scientific Cat#MPK1096 QuickExtract DNA Extraction Solution Lucigen Cat# QE09050 SE Cell Line 4DNucleofector X Kit S Lonza Cat#V4XC-1032 Illustra TempliPhi 100 amplification kit Cytiva Cat#25640010 NEB T7 HiScribe Kit New England BioLabs Cat#E2040S AAVpro Titration Kit version 2 Clontech/Takara Cat#6233 Agencourt DNAdvance Kit Beckman Coulter Cat#V10309 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 MiSeq Reagent Micro Kit v2 (300-cycles) Illumina Cat#MS-103-1002 (Continued on next page) ll OPEN ACCESS e2 Cell 186, 3983–4002.e1–e13, August 31, 2023 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Amplicon sequencing data This paper NCBI SRA: BioProject PRJNA916060 Experimental models: Cell lines Human (female): HEK293T ATCC Cat#CRL-3216 Mouse (male): N2a ATCC Cat#CCL-131 Human (female): HEK293T clone 17 ATCC Cat#CRL-11268 Primary human fibroblast (HEXA) Coriell Institute Cat#GM00221 Primary human fibroblast (UGT1A1) Coriell Institute Cat# GM09551 Primary human fibroblast (RECQL3) Coriell Institute Cat# GM02085 Primary human fibroblast (GAA) Coriell Institute Cat# GM20092 Experimental models: Organisms/strains Timed pregnant C57BL/6J mice Charles River Laboratories Cat#027 Oligonucleotides HEXA, 1278ins TATC pegRNA: mA*mU*mC*rCr UrUrCrCrArGrUrCrArGrGrGrCrCrArUrGrUrUrU rUrArGrArGrCrUrArGrArArArUrArGrCrArArGrUrU rArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCrArCr CrGrArGrUrCrGrGrUrGrCrGrUrArCrCrUrGrArAr CrCrGrUrArUrArUrCrGrUrArUrGrGrCrCrCrUrGr ArCrUrUrCrUrCrUrCrUrCrCrGrCrGrGrUrUrCr UrArUrCrUrArGrUrUrArCrGrCrGrUrUrAr ArArCrCrArArCrUrA*mG*mA*mA Integrated DNA Technologies N/A VEGFA, +2 G to A pegRNA: mG*mA*mU*rGrUr CrUrGrCrArGrGrCrCrArGrArUrGrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGr UrUrArArArArUrArArGrGrCrUrArGrUrCrCr GrUrUrArUrCrArArCrUrUrGrArArArArArGrUrGr GrCrArCrCrGrArGrUrCrGrGrUrGrCrArArUrGrUr GrCrCrArUrCrUrGrGrArGrCrArCrUrCrArUrCrUr GrGrCrCrUrGrCrArGrArArCrArArUrCrUrCrCrGr CrGrGrUrUrCrUrArUrCrUrArGrUrUrArCrGrCr GrUrUrArArArCrCrArArCrUrArGrArA*mU*mU*mU Integrated DNA Technologies N/A DNMT1, 1–15 deletion pegRNA: mG*mA*mU*rUr CrCrUrGrGrUrGrCrCrArGrArArArCrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGrUr UrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCr ArCrCrGrArGrUrCrGrGrUrGrCrArGrGrAr GrGrArArGrCrUrGrCrUrArArGrGrArCrUrArGrUrUr CrUrGrCrCrCrUrUrCrUrGrGrCrArCrCrArGrGrAr CrCrUrCrUrUrCrUrCrGrCrGrGrUrUrCrUrArUr CrUrArGrUrUrArCrGrCrGrUrUrArArArCrCrArArCrUr ArGrArA*mU*mU*mU Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Cell 186, 3983–4002.e1–e13, August 31, 2023 e3 Resource
Gel Extraction:Article Title: Phage-assisted evolution and protein engineering yield compact, efficient prime editors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains One Shot Mach1 T1 Phage-Resistant Chemically Competent E. coli Thermo Fisher Scientific Cat#C862003 E. coli S2060 Addgene #105064 Chemicals, peptides, and recombinant proteins BsaI-HFv2 New England BioLabs Cat#R3733S LguI (SapI) Thermo Fisher Scientific Cat#ER1932 T4 DNA Ligase New England BioLabs Cat#M0202S NEBuilder HiFi DNA assembly master mix New England BioLabs Cat#E2621S Dimethyl sulfoxide Sigma-Aldrich Cat#D8418-50ML Poly(ethylene glycol) 3350 Sigma-Aldrich Cat#P4338-500G DNaseI (Rnase-free) New England BioLabs Cat#M0303 Magnesium chloride solution Sigma-Aldrich Cat#M1028-10X1ML Carbenicillin Gold Biotechnology Cat#C-103 Chloramphenicol Gold Biotechnology Cat#C-105 Tetracycline Gold Biotechnology Cat#T-101 Streptomycin Gold Biotechnology Cat#S-150 L-arabinose Gold Biotechnology Cat#A-300 Glucose Sigma-Aldrich Cat#G7021 Bluo-gal Gold Biotechnology Cat#B-673-10 dNTPs New England BioLabs Cat#N0447S Lipofectamine 2000 Thermo Fisher Scientific Cat#11668019 TrypLE Thermo Fisher Scientific Cat#12605010 Proteinase K, recombinant, PCR grade Thermo Fisher Scientific Cat#11668019 SDS (10% wt/vol) Thermo Fisher Scientific Cat#15553027 DNAdvance Kit Beckman Coulter Cat#A48705 AMPure XP Beckman Coulter Cat#B23318 CleanCap Reagent AG TriLink BioTechnologies Cat#N-7113 N1 -Methylpseudouridine50 -Triphosphate TriLink BioTechnologies Cat#N-1081 LiCl Precipitation Solution (7.5 M) Thermo Fisher Scientific Cat#AM9480 DMEM, high glucose, GlutaMAX supplement Thermo Fisher Scientific Cat#10566016 Fetal bovine serum Thermo Fisher Scientific Cat#16000044 L-Glutamine Corning Cat#25-005-Cl Penicillin-Streptomycin Thermo Fisher Scientific Cat#15070063 GlutaMAX supplement Thermo Fisher Scientific Cat#35050061 N-acetyl-L-cysteine Sigma-Aldrich Cat#A7250-100G Human AB Serum Valley Biomedical Cat#HP1022HI Recombinant Human IL-2 Peprotech Cat#200-02 Lymphoprep density gradient medium STEMCELL Technologies Cat#07801 (Continued on next page) Cell 186, 3983–4002.e1–e13, August 31, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Human T-Expander CD3/CD28 Thermo Fisher Scientific Cat#11141D X-VIVO 15 Serum-free Hematopoietic Cell Medium Lonza Cat#BE02-053Q Dulbecco0s Modifi–d Eagle0s Medium – low glucose Sigma-Aldrich Cat#D5546 Eagle’s minimal essential Medium (EMEM) ATCC Cat#30-2003 Opti-MEM reduced serum medium Thermo Fisher Scientific Cat#31985070 PEG 8000 Sigma-Aldrich Cat#25322-68-3 PEG-it Virus Precipitation Solution System Biosciences Cat#LV825A-1 Salt active nuclease ArcticZymes Cat#70910-202 0.9% NaCl Fresenius Kabi Cat#918610 BSA NEB Cat#B9000S Vybrant DyeCycle Ruby Thermo Fisher Cat#V10309 EZ-PREP buffer Sigma-Aldrich #NUC-101 Critical commercial assays Phusion U Multiplex PCR Master Mix Thermo Fisher Scientific Cat#F562L Q5 High-Fidelity 2 x Master Mix New England BioLabs Cat#M0492L Phusion Green Hot Start II High-Fidelity DNA Polymerase Thermo Fisher Scientific Cat#F537L QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 QIAGEN Plasmid Plus Midi Kit QIAGEN Cat#12943 QIAprep Spin Miniprep Kit QIAGEN Cat#27106 Qiagen Plasmid Plus 96 Miniprep Kit QIAGEN Cat#16181 EasySep Human T cell Isolation Kit STEMCELL Technologies Cat#17951 Neon Transfection System Thermo Fisher Scientific Cat#MPK1096 QuickExtract DNA Extraction Solution Lucigen Cat# QE09050 SE Cell Line 4DNucleofector X Kit S Lonza Cat#V4XC-1032 Illustra TempliPhi 100 amplification kit Cytiva Cat#25640010 NEB T7 HiScribe Kit New England BioLabs Cat#E2040S AAVpro Titration Kit version 2 Clontech/Takara Cat#6233 Agencourt DNAdvance Kit Beckman Coulter Cat#V10309 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 MiSeq Reagent Micro Kit v2 (300-cycles) Illumina Cat#MS-103-1002 (Continued on next page) ll OPEN ACCESS e2 Cell 186, 3983–4002.e1–e13, August 31, 2023 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Amplicon sequencing data This paper NCBI SRA: BioProject PRJNA916060 Experimental models: Cell lines Human (female): HEK293T ATCC Cat#CRL-3216 Mouse (male): N2a ATCC Cat#CCL-131 Human (female): HEK293T clone 17 ATCC Cat#CRL-11268 Primary human fibroblast (HEXA) Coriell Institute Cat#GM00221 Primary human fibroblast (UGT1A1) Coriell Institute Cat# GM09551 Primary human fibroblast (RECQL3) Coriell Institute Cat# GM02085 Primary human fibroblast (GAA) Coriell Institute Cat# GM20092 Experimental models: Organisms/strains Timed pregnant C57BL/6J mice Charles River Laboratories Cat#027 Oligonucleotides HEXA, 1278ins TATC pegRNA: mA*mU*mC*rCr UrUrCrCrArGrUrCrArGrGrGrCrCrArUrGrUrUrU rUrArGrArGrCrUrArGrArArArUrArGrCrArArGrUrU rArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCrArCr CrGrArGrUrCrGrGrUrGrCrGrUrArCrCrUrGrArAr CrCrGrUrArUrArUrCrGrUrArUrGrGrCrCrCrUrGr ArCrUrUrCrUrCrUrCrUrCrCrGrCrGrGrUrUrCr UrArUrCrUrArGrUrUrArCrGrCrGrUrUrAr ArArCrCrArArCrUrA*mG*mA*mA Integrated DNA Technologies N/A VEGFA, +2 G to A pegRNA: mG*mA*mU*rGrUr CrUrGrCrArGrGrCrCrArGrArUrGrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGr UrUrArArArArUrArArGrGrCrUrArGrUrCrCr GrUrUrArUrCrArArCrUrUrGrArArArArArGrUrGr GrCrArCrCrGrArGrUrCrGrGrUrGrCrArArUrGrUr GrCrCrArUrCrUrGrGrArGrCrArCrUrCrArUrCrUr GrGrCrCrUrGrCrArGrArArCrArArUrCrUrCrCrGr CrGrGrUrUrCrUrArUrCrUrArGrUrUrArCrGrCr GrUrUrArArArCrCrArArCrUrArGrArA*mU*mU*mU Integrated DNA Technologies N/A DNMT1, 1–15 deletion pegRNA: mG*mA*mU*rUr CrCrUrGrGrUrGrCrCrArGrArArArCrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGrUr UrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCr ArCrCrGrArGrUrCrGrGrUrGrCrArGrGrAr GrGrArArGrCrUrGrCrUrArArGrGrArCrUrArGrUrUr CrUrGrCrCrCrUrUrCrUrGrGrCrArCrCrArGrGrAr CrCrUrCrUrUrCrUrCrGrCrGrGrUrUrCrUrArUr CrUrArGrUrUrArCrGrCrGrUrUrArArArCrCrArArCrUr ArGrArA*mU*mU*mU Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Cell 186, 3983–4002.e1–e13, August 31, 2023 e3 Resource
Plasmid Preparation:Article Title: Phage-assisted evolution and protein engineering yield compact, efficient prime editors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains One Shot Mach1 T1 Phage-Resistant Chemically Competent E. coli Thermo Fisher Scientific Cat#C862003 E. coli S2060 Addgene #105064 Chemicals, peptides, and recombinant proteins BsaI-HFv2 New England BioLabs Cat#R3733S LguI (SapI) Thermo Fisher Scientific Cat#ER1932 T4 DNA Ligase New England BioLabs Cat#M0202S NEBuilder HiFi DNA assembly master mix New England BioLabs Cat#E2621S Dimethyl sulfoxide Sigma-Aldrich Cat#D8418-50ML Poly(ethylene glycol) 3350 Sigma-Aldrich Cat#P4338-500G DNaseI (Rnase-free) New England BioLabs Cat#M0303 Magnesium chloride solution Sigma-Aldrich Cat#M1028-10X1ML Carbenicillin Gold Biotechnology Cat#C-103 Chloramphenicol Gold Biotechnology Cat#C-105 Tetracycline Gold Biotechnology Cat#T-101 Streptomycin Gold Biotechnology Cat#S-150 L-arabinose Gold Biotechnology Cat#A-300 Glucose Sigma-Aldrich Cat#G7021 Bluo-gal Gold Biotechnology Cat#B-673-10 dNTPs New England BioLabs Cat#N0447S Lipofectamine 2000 Thermo Fisher Scientific Cat#11668019 TrypLE Thermo Fisher Scientific Cat#12605010 Proteinase K, recombinant, PCR grade Thermo Fisher Scientific Cat#11668019 SDS (10% wt/vol) Thermo Fisher Scientific Cat#15553027 DNAdvance Kit Beckman Coulter Cat#A48705 AMPure XP Beckman Coulter Cat#B23318 CleanCap Reagent AG TriLink BioTechnologies Cat#N-7113 N1 -Methylpseudouridine50 -Triphosphate TriLink BioTechnologies Cat#N-1081 LiCl Precipitation Solution (7.5 M) Thermo Fisher Scientific Cat#AM9480 DMEM, high glucose, GlutaMAX supplement Thermo Fisher Scientific Cat#10566016 Fetal bovine serum Thermo Fisher Scientific Cat#16000044 L-Glutamine Corning Cat#25-005-Cl Penicillin-Streptomycin Thermo Fisher Scientific Cat#15070063 GlutaMAX supplement Thermo Fisher Scientific Cat#35050061 N-acetyl-L-cysteine Sigma-Aldrich Cat#A7250-100G Human AB Serum Valley Biomedical Cat#HP1022HI Recombinant Human IL-2 Peprotech Cat#200-02 Lymphoprep density gradient medium STEMCELL Technologies Cat#07801 (Continued on next page) Cell 186, 3983–4002.e1–e13, August 31, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Human T-Expander CD3/CD28 Thermo Fisher Scientific Cat#11141D X-VIVO 15 Serum-free Hematopoietic Cell Medium Lonza Cat#BE02-053Q Dulbecco0s Modifi–d Eagle0s Medium – low glucose Sigma-Aldrich Cat#D5546 Eagle’s minimal essential Medium (EMEM) ATCC Cat#30-2003 Opti-MEM reduced serum medium Thermo Fisher Scientific Cat#31985070 PEG 8000 Sigma-Aldrich Cat#25322-68-3 PEG-it Virus Precipitation Solution System Biosciences Cat#LV825A-1 Salt active nuclease ArcticZymes Cat#70910-202 0.9% NaCl Fresenius Kabi Cat#918610 BSA NEB Cat#B9000S Vybrant DyeCycle Ruby Thermo Fisher Cat#V10309 EZ-PREP buffer Sigma-Aldrich #NUC-101 Critical commercial assays Phusion U Multiplex PCR Master Mix Thermo Fisher Scientific Cat#F562L Q5 High-Fidelity 2 x Master Mix New England BioLabs Cat#M0492L Phusion Green Hot Start II High-Fidelity DNA Polymerase Thermo Fisher Scientific Cat#F537L QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 QIAGEN Plasmid Plus Midi Kit QIAGEN Cat#12943 QIAprep Spin Miniprep Kit QIAGEN Cat#27106 Qiagen Plasmid Plus 96 Miniprep Kit QIAGEN Cat#16181 EasySep Human T cell Isolation Kit STEMCELL Technologies Cat#17951 Neon Transfection System Thermo Fisher Scientific Cat#MPK1096 QuickExtract DNA Extraction Solution Lucigen Cat# QE09050 SE Cell Line 4DNucleofector X Kit S Lonza Cat#V4XC-1032 Illustra TempliPhi 100 amplification kit Cytiva Cat#25640010 NEB T7 HiScribe Kit New England BioLabs Cat#E2040S AAVpro Titration Kit version 2 Clontech/Takara Cat#6233 Agencourt DNAdvance Kit Beckman Coulter Cat#V10309 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 MiSeq Reagent Micro Kit v2 (300-cycles) Illumina Cat#MS-103-1002 (Continued on next page) ll OPEN ACCESS e2 Cell 186, 3983–4002.e1–e13, August 31, 2023 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Amplicon sequencing data This paper NCBI SRA: BioProject PRJNA916060 Experimental models: Cell lines Human (female): HEK293T ATCC Cat#CRL-3216 Mouse (male): N2a ATCC Cat#CCL-131 Human (female): HEK293T clone 17 ATCC Cat#CRL-11268 Primary human fibroblast (HEXA) Coriell Institute Cat#GM00221 Primary human fibroblast (UGT1A1) Coriell Institute Cat# GM09551 Primary human fibroblast (RECQL3) Coriell Institute Cat# GM02085 Primary human fibroblast (GAA) Coriell Institute Cat# GM20092 Experimental models: Organisms/strains Timed pregnant C57BL/6J mice Charles River Laboratories Cat#027 Oligonucleotides HEXA, 1278ins TATC pegRNA: mA*mU*mC*rCr UrUrCrCrArGrUrCrArGrGrGrCrCrArUrGrUrUrU rUrArGrArGrCrUrArGrArArArUrArGrCrArArGrUrU rArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCrArCr CrGrArGrUrCrGrGrUrGrCrGrUrArCrCrUrGrArAr CrCrGrUrArUrArUrCrGrUrArUrGrGrCrCrCrUrGr ArCrUrUrCrUrCrUrCrUrCrCrGrCrGrGrUrUrCr UrArUrCrUrArGrUrUrArCrGrCrGrUrUrAr ArArCrCrArArCrUrA*mG*mA*mA Integrated DNA Technologies N/A VEGFA, +2 G to A pegRNA: mG*mA*mU*rGrUr CrUrGrCrArGrGrCrCrArGrArUrGrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGr UrUrArArArArUrArArGrGrCrUrArGrUrCrCr GrUrUrArUrCrArArCrUrUrGrArArArArArGrUrGr GrCrArCrCrGrArGrUrCrGrGrUrGrCrArArUrGrUr GrCrCrArUrCrUrGrGrArGrCrArCrUrCrArUrCrUr GrGrCrCrUrGrCrArGrArArCrArArUrCrUrCrCrGr CrGrGrUrUrCrUrArUrCrUrArGrUrUrArCrGrCr GrUrUrArArArCrCrArArCrUrArGrArA*mU*mU*mU Integrated DNA Technologies N/A DNMT1, 1–15 deletion pegRNA: mG*mA*mU*rUr CrCrUrGrGrUrGrCrCrArGrArArArCrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGrUr UrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCr ArCrCrGrArGrUrCrGrGrUrGrCrArGrGrAr GrGrArArGrCrUrGrCrUrArArGrGrArCrUrArGrUrUr CrUrGrCrCrCrUrUrCrUrGrGrCrArCrCrArGrGrAr CrCrUrCrUrUrCrUrCrGrCrGrGrUrUrCrUrArUr CrUrArGrUrUrArCrGrCrGrUrUrArArArCrCrArArCrUr ArGrArA*mU*mU*mU Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Cell 186, 3983–4002.e1–e13, August 31, 2023 e3 Resource
Cell Isolation:Article Title: Phage-assisted evolution and protein engineering yield compact, efficient prime editors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains One Shot Mach1 T1 Phage-Resistant Chemically Competent E. coli Thermo Fisher Scientific Cat#C862003 E. coli S2060 Addgene #105064 Chemicals, peptides, and recombinant proteins BsaI-HFv2 New England BioLabs Cat#R3733S LguI (SapI) Thermo Fisher Scientific Cat#ER1932 T4 DNA Ligase New England BioLabs Cat#M0202S NEBuilder HiFi DNA assembly master mix New England BioLabs Cat#E2621S Dimethyl sulfoxide Sigma-Aldrich Cat#D8418-50ML Poly(ethylene glycol) 3350 Sigma-Aldrich Cat#P4338-500G DNaseI (Rnase-free) New England BioLabs Cat#M0303 Magnesium chloride solution Sigma-Aldrich Cat#M1028-10X1ML Carbenicillin Gold Biotechnology Cat#C-103 Chloramphenicol Gold Biotechnology Cat#C-105 Tetracycline Gold Biotechnology Cat#T-101 Streptomycin Gold Biotechnology Cat#S-150 L-arabinose Gold Biotechnology Cat#A-300 Glucose Sigma-Aldrich Cat#G7021 Bluo-gal Gold Biotechnology Cat#B-673-10 dNTPs New England BioLabs Cat#N0447S Lipofectamine 2000 Thermo Fisher Scientific Cat#11668019 TrypLE Thermo Fisher Scientific Cat#12605010 Proteinase K, recombinant, PCR grade Thermo Fisher Scientific Cat#11668019 SDS (10% wt/vol) Thermo Fisher Scientific Cat#15553027 DNAdvance Kit Beckman Coulter Cat#A48705 AMPure XP Beckman Coulter Cat#B23318 CleanCap Reagent AG TriLink BioTechnologies Cat#N-7113 N1 -Methylpseudouridine50 -Triphosphate TriLink BioTechnologies Cat#N-1081 LiCl Precipitation Solution (7.5 M) Thermo Fisher Scientific Cat#AM9480 DMEM, high glucose, GlutaMAX supplement Thermo Fisher Scientific Cat#10566016 Fetal bovine serum Thermo Fisher Scientific Cat#16000044 L-Glutamine Corning Cat#25-005-Cl Penicillin-Streptomycin Thermo Fisher Scientific Cat#15070063 GlutaMAX supplement Thermo Fisher Scientific Cat#35050061 N-acetyl-L-cysteine Sigma-Aldrich Cat#A7250-100G Human AB Serum Valley Biomedical Cat#HP1022HI Recombinant Human IL-2 Peprotech Cat#200-02 Lymphoprep density gradient medium STEMCELL Technologies Cat#07801 (Continued on next page) Cell 186, 3983–4002.e1–e13, August 31, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Human T-Expander CD3/CD28 Thermo Fisher Scientific Cat#11141D X-VIVO 15 Serum-free Hematopoietic Cell Medium Lonza Cat#BE02-053Q Dulbecco0s Modifi–d Eagle0s Medium – low glucose Sigma-Aldrich Cat#D5546 Eagle’s minimal essential Medium (EMEM) ATCC Cat#30-2003 Opti-MEM reduced serum medium Thermo Fisher Scientific Cat#31985070 PEG 8000 Sigma-Aldrich Cat#25322-68-3 PEG-it Virus Precipitation Solution System Biosciences Cat#LV825A-1 Salt active nuclease ArcticZymes Cat#70910-202 0.9% NaCl Fresenius Kabi Cat#918610 BSA NEB Cat#B9000S Vybrant DyeCycle Ruby Thermo Fisher Cat#V10309 EZ-PREP buffer Sigma-Aldrich #NUC-101 Critical commercial assays Phusion U Multiplex PCR Master Mix Thermo Fisher Scientific Cat#F562L Q5 High-Fidelity 2 x Master Mix New England BioLabs Cat#M0492L Phusion Green Hot Start II High-Fidelity DNA Polymerase Thermo Fisher Scientific Cat#F537L QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 QIAGEN Plasmid Plus Midi Kit QIAGEN Cat#12943 QIAprep Spin Miniprep Kit QIAGEN Cat#27106 Qiagen Plasmid Plus 96 Miniprep Kit QIAGEN Cat#16181 EasySep Human T cell Isolation Kit STEMCELL Technologies Cat#17951 Neon Transfection System Thermo Fisher Scientific Cat#MPK1096 QuickExtract DNA Extraction Solution Lucigen Cat# QE09050 SE Cell Line 4DNucleofector X Kit S Lonza Cat#V4XC-1032 Illustra TempliPhi 100 amplification kit Cytiva Cat#25640010 NEB T7 HiScribe Kit New England BioLabs Cat#E2040S AAVpro Titration Kit version 2 Clontech/Takara Cat#6233 Agencourt DNAdvance Kit Beckman Coulter Cat#V10309 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 MiSeq Reagent Micro Kit v2 (300-cycles) Illumina Cat#MS-103-1002 (Continued on next page) ll OPEN ACCESS e2 Cell 186, 3983–4002.e1–e13, August 31, 2023 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Amplicon sequencing data This paper NCBI SRA: BioProject PRJNA916060 Experimental models: Cell lines Human (female): HEK293T ATCC Cat#CRL-3216 Mouse (male): N2a ATCC Cat#CCL-131 Human (female): HEK293T clone 17 ATCC Cat#CRL-11268 Primary human fibroblast (HEXA) Coriell Institute Cat#GM00221 Primary human fibroblast (UGT1A1) Coriell Institute Cat# GM09551 Primary human fibroblast (RECQL3) Coriell Institute Cat# GM02085 Primary human fibroblast (GAA) Coriell Institute Cat# GM20092 Experimental models: Organisms/strains Timed pregnant C57BL/6J mice Charles River Laboratories Cat#027 Oligonucleotides HEXA, 1278ins TATC pegRNA: mA*mU*mC*rCr UrUrCrCrArGrUrCrArGrGrGrCrCrArUrGrUrUrU rUrArGrArGrCrUrArGrArArArUrArGrCrArArGrUrU rArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCrArCr CrGrArGrUrCrGrGrUrGrCrGrUrArCrCrUrGrArAr CrCrGrUrArUrArUrCrGrUrArUrGrGrCrCrCrUrGr ArCrUrUrCrUrCrUrCrUrCrCrGrCrGrGrUrUrCr UrArUrCrUrArGrUrUrArCrGrCrGrUrUrAr ArArCrCrArArCrUrA*mG*mA*mA Integrated DNA Technologies N/A VEGFA, +2 G to A pegRNA: mG*mA*mU*rGrUr CrUrGrCrArGrGrCrCrArGrArUrGrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGr UrUrArArArArUrArArGrGrCrUrArGrUrCrCr GrUrUrArUrCrArArCrUrUrGrArArArArArGrUrGr GrCrArCrCrGrArGrUrCrGrGrUrGrCrArArUrGrUr GrCrCrArUrCrUrGrGrArGrCrArCrUrCrArUrCrUr GrGrCrCrUrGrCrArGrArArCrArArUrCrUrCrCrGr CrGrGrUrUrCrUrArUrCrUrArGrUrUrArCrGrCr GrUrUrArArArCrCrArArCrUrArGrArA*mU*mU*mU Integrated DNA Technologies N/A DNMT1, 1–15 deletion pegRNA: mG*mA*mU*rUr CrCrUrGrGrUrGrCrCrArGrArArArCrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGrUr UrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCr ArCrCrGrArGrUrCrGrGrUrGrCrArGrGrAr GrGrArArGrCrUrGrCrUrArArGrGrArCrUrArGrUrUr CrUrGrCrCrCrUrUrCrUrGrGrCrArCrCrArGrGrAr CrCrUrCrUrUrCrUrCrGrCrGrGrUrUrCrUrArUr CrUrArGrUrUrArCrGrCrGrUrUrArArArCrCrArArCrUr ArGrArA*mU*mU*mU Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Cell 186, 3983–4002.e1–e13, August 31, 2023 e3 Resource
Transfection:Article Title: Phage-assisted evolution and protein engineering yield compact, efficient prime editors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains One Shot Mach1 T1 Phage-Resistant Chemically Competent E. coli Thermo Fisher Scientific Cat#C862003 E. coli S2060 Addgene #105064 Chemicals, peptides, and recombinant proteins BsaI-HFv2 New England BioLabs Cat#R3733S LguI (SapI) Thermo Fisher Scientific Cat#ER1932 T4 DNA Ligase New England BioLabs Cat#M0202S NEBuilder HiFi DNA assembly master mix New England BioLabs Cat#E2621S Dimethyl sulfoxide Sigma-Aldrich Cat#D8418-50ML Poly(ethylene glycol) 3350 Sigma-Aldrich Cat#P4338-500G DNaseI (Rnase-free) New England BioLabs Cat#M0303 Magnesium chloride solution Sigma-Aldrich Cat#M1028-10X1ML Carbenicillin Gold Biotechnology Cat#C-103 Chloramphenicol Gold Biotechnology Cat#C-105 Tetracycline Gold Biotechnology Cat#T-101 Streptomycin Gold Biotechnology Cat#S-150 L-arabinose Gold Biotechnology Cat#A-300 Glucose Sigma-Aldrich Cat#G7021 Bluo-gal Gold Biotechnology Cat#B-673-10 dNTPs New England BioLabs Cat#N0447S Lipofectamine 2000 Thermo Fisher Scientific Cat#11668019 TrypLE Thermo Fisher Scientific Cat#12605010 Proteinase K, recombinant, PCR grade Thermo Fisher Scientific Cat#11668019 SDS (10% wt/vol) Thermo Fisher Scientific Cat#15553027 DNAdvance Kit Beckman Coulter Cat#A48705 AMPure XP Beckman Coulter Cat#B23318 CleanCap Reagent AG TriLink BioTechnologies Cat#N-7113 N1 -Methylpseudouridine50 -Triphosphate TriLink BioTechnologies Cat#N-1081 LiCl Precipitation Solution (7.5 M) Thermo Fisher Scientific Cat#AM9480 DMEM, high glucose, GlutaMAX supplement Thermo Fisher Scientific Cat#10566016 Fetal bovine serum Thermo Fisher Scientific Cat#16000044 L-Glutamine Corning Cat#25-005-Cl Penicillin-Streptomycin Thermo Fisher Scientific Cat#15070063 GlutaMAX supplement Thermo Fisher Scientific Cat#35050061 N-acetyl-L-cysteine Sigma-Aldrich Cat#A7250-100G Human AB Serum Valley Biomedical Cat#HP1022HI Recombinant Human IL-2 Peprotech Cat#200-02 Lymphoprep density gradient medium STEMCELL Technologies Cat#07801 (Continued on next page) Cell 186, 3983–4002.e1–e13, August 31, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Human T-Expander CD3/CD28 Thermo Fisher Scientific Cat#11141D X-VIVO 15 Serum-free Hematopoietic Cell Medium Lonza Cat#BE02-053Q Dulbecco0s Modifi–d Eagle0s Medium – low glucose Sigma-Aldrich Cat#D5546 Eagle’s minimal essential Medium (EMEM) ATCC Cat#30-2003 Opti-MEM reduced serum medium Thermo Fisher Scientific Cat#31985070 PEG 8000 Sigma-Aldrich Cat#25322-68-3 PEG-it Virus Precipitation Solution System Biosciences Cat#LV825A-1 Salt active nuclease ArcticZymes Cat#70910-202 0.9% NaCl Fresenius Kabi Cat#918610 BSA NEB Cat#B9000S Vybrant DyeCycle Ruby Thermo Fisher Cat#V10309 EZ-PREP buffer Sigma-Aldrich #NUC-101 Critical commercial assays Phusion U Multiplex PCR Master Mix Thermo Fisher Scientific Cat#F562L Q5 High-Fidelity 2 x Master Mix New England BioLabs Cat#M0492L Phusion Green Hot Start II High-Fidelity DNA Polymerase Thermo Fisher Scientific Cat#F537L QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 QIAGEN Plasmid Plus Midi Kit QIAGEN Cat#12943 QIAprep Spin Miniprep Kit QIAGEN Cat#27106 Qiagen Plasmid Plus 96 Miniprep Kit QIAGEN Cat#16181 EasySep Human T cell Isolation Kit STEMCELL Technologies Cat#17951 Neon Transfection System Thermo Fisher Scientific Cat#MPK1096 QuickExtract DNA Extraction Solution Lucigen Cat# QE09050 SE Cell Line 4DNucleofector X Kit S Lonza Cat#V4XC-1032 Illustra TempliPhi 100 amplification kit Cytiva Cat#25640010 NEB T7 HiScribe Kit New England BioLabs Cat#E2040S AAVpro Titration Kit version 2 Clontech/Takara Cat#6233 Agencourt DNAdvance Kit Beckman Coulter Cat#V10309 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 MiSeq Reagent Micro Kit v2 (300-cycles) Illumina Cat#MS-103-1002 (Continued on next page) ll OPEN ACCESS e2 Cell 186, 3983–4002.e1–e13, August 31, 2023 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Amplicon sequencing data This paper NCBI SRA: BioProject PRJNA916060 Experimental models: Cell lines Human (female): HEK293T ATCC Cat#CRL-3216 Mouse (male): N2a ATCC Cat#CCL-131 Human (female): HEK293T clone 17 ATCC Cat#CRL-11268 Primary human fibroblast (HEXA) Coriell Institute Cat#GM00221 Primary human fibroblast (UGT1A1) Coriell Institute Cat# GM09551 Primary human fibroblast (RECQL3) Coriell Institute Cat# GM02085 Primary human fibroblast (GAA) Coriell Institute Cat# GM20092 Experimental models: Organisms/strains Timed pregnant C57BL/6J mice Charles River Laboratories Cat#027 Oligonucleotides HEXA, 1278ins TATC pegRNA: mA*mU*mC*rCr UrUrCrCrArGrUrCrArGrGrGrCrCrArUrGrUrUrU rUrArGrArGrCrUrArGrArArArUrArGrCrArArGrUrU rArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCrArCr CrGrArGrUrCrGrGrUrGrCrGrUrArCrCrUrGrArAr CrCrGrUrArUrArUrCrGrUrArUrGrGrCrCrCrUrGr ArCrUrUrCrUrCrUrCrUrCrCrGrCrGrGrUrUrCr UrArUrCrUrArGrUrUrArCrGrCrGrUrUrAr ArArCrCrArArCrUrA*mG*mA*mA Integrated DNA Technologies N/A VEGFA, +2 G to A pegRNA: mG*mA*mU*rGrUr CrUrGrCrArGrGrCrCrArGrArUrGrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGr UrUrArArArArUrArArGrGrCrUrArGrUrCrCr GrUrUrArUrCrArArCrUrUrGrArArArArArGrUrGr GrCrArCrCrGrArGrUrCrGrGrUrGrCrArArUrGrUr GrCrCrArUrCrUrGrGrArGrCrArCrUrCrArUrCrUr GrGrCrCrUrGrCrArGrArArCrArArUrCrUrCrCrGr CrGrGrUrUrCrUrArUrCrUrArGrUrUrArCrGrCr GrUrUrArArArCrCrArArCrUrArGrArA*mU*mU*mU Integrated DNA Technologies N/A DNMT1, 1–15 deletion pegRNA: mG*mA*mU*rUr CrCrUrGrGrUrGrCrCrArGrArArArCrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGrUr UrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCr ArCrCrGrArGrUrCrGrGrUrGrCrArGrGrAr GrGrArArGrCrUrGrCrUrArArGrGrArCrUrArGrUrUr CrUrGrCrCrCrUrUrCrUrGrGrCrArCrCrArGrGrAr CrCrUrCrUrUrCrUrCrGrCrGrGrUrUrCrUrArUr CrUrArGrUrUrArCrGrCrGrUrUrArArArCrCrArArCrUr ArGrArA*mU*mU*mU Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Cell 186, 3983–4002.e1–e13, August 31, 2023 e3 Resource
DNA Extraction:Article Title: Phage-assisted evolution and protein engineering yield compact, efficient prime editors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains One Shot Mach1 T1 Phage-Resistant Chemically Competent E. coli Thermo Fisher Scientific Cat#C862003 E. coli S2060 Addgene #105064 Chemicals, peptides, and recombinant proteins BsaI-HFv2 New England BioLabs Cat#R3733S LguI (SapI) Thermo Fisher Scientific Cat#ER1932 T4 DNA Ligase New England BioLabs Cat#M0202S NEBuilder HiFi DNA assembly master mix New England BioLabs Cat#E2621S Dimethyl sulfoxide Sigma-Aldrich Cat#D8418-50ML Poly(ethylene glycol) 3350 Sigma-Aldrich Cat#P4338-500G DNaseI (Rnase-free) New England BioLabs Cat#M0303 Magnesium chloride solution Sigma-Aldrich Cat#M1028-10X1ML Carbenicillin Gold Biotechnology Cat#C-103 Chloramphenicol Gold Biotechnology Cat#C-105 Tetracycline Gold Biotechnology Cat#T-101 Streptomycin Gold Biotechnology Cat#S-150 L-arabinose Gold Biotechnology Cat#A-300 Glucose Sigma-Aldrich Cat#G7021 Bluo-gal Gold Biotechnology Cat#B-673-10 dNTPs New England BioLabs Cat#N0447S Lipofectamine 2000 Thermo Fisher Scientific Cat#11668019 TrypLE Thermo Fisher Scientific Cat#12605010 Proteinase K, recombinant, PCR grade Thermo Fisher Scientific Cat#11668019 SDS (10% wt/vol) Thermo Fisher Scientific Cat#15553027 DNAdvance Kit Beckman Coulter Cat#A48705 AMPure XP Beckman Coulter Cat#B23318 CleanCap Reagent AG TriLink BioTechnologies Cat#N-7113 N1 -Methylpseudouridine50 -Triphosphate TriLink BioTechnologies Cat#N-1081 LiCl Precipitation Solution (7.5 M) Thermo Fisher Scientific Cat#AM9480 DMEM, high glucose, GlutaMAX supplement Thermo Fisher Scientific Cat#10566016 Fetal bovine serum Thermo Fisher Scientific Cat#16000044 L-Glutamine Corning Cat#25-005-Cl Penicillin-Streptomycin Thermo Fisher Scientific Cat#15070063 GlutaMAX supplement Thermo Fisher Scientific Cat#35050061 N-acetyl-L-cysteine Sigma-Aldrich Cat#A7250-100G Human AB Serum Valley Biomedical Cat#HP1022HI Recombinant Human IL-2 Peprotech Cat#200-02 Lymphoprep density gradient medium STEMCELL Technologies Cat#07801 (Continued on next page) Cell 186, 3983–4002.e1–e13, August 31, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Human T-Expander CD3/CD28 Thermo Fisher Scientific Cat#11141D X-VIVO 15 Serum-free Hematopoietic Cell Medium Lonza Cat#BE02-053Q Dulbecco0s Modifi–d Eagle0s Medium – low glucose Sigma-Aldrich Cat#D5546 Eagle’s minimal essential Medium (EMEM) ATCC Cat#30-2003 Opti-MEM reduced serum medium Thermo Fisher Scientific Cat#31985070 PEG 8000 Sigma-Aldrich Cat#25322-68-3 PEG-it Virus Precipitation Solution System Biosciences Cat#LV825A-1 Salt active nuclease ArcticZymes Cat#70910-202 0.9% NaCl Fresenius Kabi Cat#918610 BSA NEB Cat#B9000S Vybrant DyeCycle Ruby Thermo Fisher Cat#V10309 EZ-PREP buffer Sigma-Aldrich #NUC-101 Critical commercial assays Phusion U Multiplex PCR Master Mix Thermo Fisher Scientific Cat#F562L Q5 High-Fidelity 2 x Master Mix New England BioLabs Cat#M0492L Phusion Green Hot Start II High-Fidelity DNA Polymerase Thermo Fisher Scientific Cat#F537L QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 QIAGEN Plasmid Plus Midi Kit QIAGEN Cat#12943 QIAprep Spin Miniprep Kit QIAGEN Cat#27106 Qiagen Plasmid Plus 96 Miniprep Kit QIAGEN Cat#16181 EasySep Human T cell Isolation Kit STEMCELL Technologies Cat#17951 Neon Transfection System Thermo Fisher Scientific Cat#MPK1096 QuickExtract DNA Extraction Solution Lucigen Cat# QE09050 SE Cell Line 4DNucleofector X Kit S Lonza Cat#V4XC-1032 Illustra TempliPhi 100 amplification kit Cytiva Cat#25640010 NEB T7 HiScribe Kit New England BioLabs Cat#E2040S AAVpro Titration Kit version 2 Clontech/Takara Cat#6233 Agencourt DNAdvance Kit Beckman Coulter Cat#V10309 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 MiSeq Reagent Micro Kit v2 (300-cycles) Illumina Cat#MS-103-1002 (Continued on next page) ll OPEN ACCESS e2 Cell 186, 3983–4002.e1–e13, August 31, 2023 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Amplicon sequencing data This paper NCBI SRA: BioProject PRJNA916060 Experimental models: Cell lines Human (female): HEK293T ATCC Cat#CRL-3216 Mouse (male): N2a ATCC Cat#CCL-131 Human (female): HEK293T clone 17 ATCC Cat#CRL-11268 Primary human fibroblast (HEXA) Coriell Institute Cat#GM00221 Primary human fibroblast (UGT1A1) Coriell Institute Cat# GM09551 Primary human fibroblast (RECQL3) Coriell Institute Cat# GM02085 Primary human fibroblast (GAA) Coriell Institute Cat# GM20092 Experimental models: Organisms/strains Timed pregnant C57BL/6J mice Charles River Laboratories Cat#027 Oligonucleotides HEXA, 1278ins TATC pegRNA: mA*mU*mC*rCr UrUrCrCrArGrUrCrArGrGrGrCrCrArUrGrUrUrU rUrArGrArGrCrUrArGrArArArUrArGrCrArArGrUrU rArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCrArCr CrGrArGrUrCrGrGrUrGrCrGrUrArCrCrUrGrArAr CrCrGrUrArUrArUrCrGrUrArUrGrGrCrCrCrUrGr ArCrUrUrCrUrCrUrCrUrCrCrGrCrGrGrUrUrCr UrArUrCrUrArGrUrUrArCrGrCrGrUrUrAr ArArCrCrArArCrUrA*mG*mA*mA Integrated DNA Technologies N/A VEGFA, +2 G to A pegRNA: mG*mA*mU*rGrUr CrUrGrCrArGrGrCrCrArGrArUrGrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGr UrUrArArArArUrArArGrGrCrUrArGrUrCrCr GrUrUrArUrCrArArCrUrUrGrArArArArArGrUrGr GrCrArCrCrGrArGrUrCrGrGrUrGrCrArArUrGrUr GrCrCrArUrCrUrGrGrArGrCrArCrUrCrArUrCrUr GrGrCrCrUrGrCrArGrArArCrArArUrCrUrCrCrGr CrGrGrUrUrCrUrArUrCrUrArGrUrUrArCrGrCr GrUrUrArArArCrCrArArCrUrArGrArA*mU*mU*mU Integrated DNA Technologies N/A DNMT1, 1–15 deletion pegRNA: mG*mA*mU*rUr CrCrUrGrGrUrGrCrCrArGrArArArCrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGrUr UrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCr ArCrCrGrArGrUrCrGrGrUrGrCrArGrGrAr GrGrArArGrCrUrGrCrUrArArGrGrArCrUrArGrUrUr CrUrGrCrCrCrUrUrCrUrGrGrCrArCrCrArGrGrAr CrCrUrCrUrUrCrUrCrGrCrGrGrUrUrCrUrArUr CrUrArGrUrUrArCrGrCrGrUrUrArArArCrCrArArCrUr ArGrArA*mU*mU*mU Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Cell 186, 3983–4002.e1–e13, August 31, 2023 e3 Resource
Amplification:Article Title: Phage-assisted evolution and protein engineering yield compact, efficient prime editors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains One Shot Mach1 T1 Phage-Resistant Chemically Competent E. coli Thermo Fisher Scientific Cat#C862003 E. coli S2060 Addgene #105064 Chemicals, peptides, and recombinant proteins BsaI-HFv2 New England BioLabs Cat#R3733S LguI (SapI) Thermo Fisher Scientific Cat#ER1932 T4 DNA Ligase New England BioLabs Cat#M0202S NEBuilder HiFi DNA assembly master mix New England BioLabs Cat#E2621S Dimethyl sulfoxide Sigma-Aldrich Cat#D8418-50ML Poly(ethylene glycol) 3350 Sigma-Aldrich Cat#P4338-500G DNaseI (Rnase-free) New England BioLabs Cat#M0303 Magnesium chloride solution Sigma-Aldrich Cat#M1028-10X1ML Carbenicillin Gold Biotechnology Cat#C-103 Chloramphenicol Gold Biotechnology Cat#C-105 Tetracycline Gold Biotechnology Cat#T-101 Streptomycin Gold Biotechnology Cat#S-150 L-arabinose Gold Biotechnology Cat#A-300 Glucose Sigma-Aldrich Cat#G7021 Bluo-gal Gold Biotechnology Cat#B-673-10 dNTPs New England BioLabs Cat#N0447S Lipofectamine 2000 Thermo Fisher Scientific Cat#11668019 TrypLE Thermo Fisher Scientific Cat#12605010 Proteinase K, recombinant, PCR grade Thermo Fisher Scientific Cat#11668019 SDS (10% wt/vol) Thermo Fisher Scientific Cat#15553027 DNAdvance Kit Beckman Coulter Cat#A48705 AMPure XP Beckman Coulter Cat#B23318 CleanCap Reagent AG TriLink BioTechnologies Cat#N-7113 N1 -Methylpseudouridine50 -Triphosphate TriLink BioTechnologies Cat#N-1081 LiCl Precipitation Solution (7.5 M) Thermo Fisher Scientific Cat#AM9480 DMEM, high glucose, GlutaMAX supplement Thermo Fisher Scientific Cat#10566016 Fetal bovine serum Thermo Fisher Scientific Cat#16000044 L-Glutamine Corning Cat#25-005-Cl Penicillin-Streptomycin Thermo Fisher Scientific Cat#15070063 GlutaMAX supplement Thermo Fisher Scientific Cat#35050061 N-acetyl-L-cysteine Sigma-Aldrich Cat#A7250-100G Human AB Serum Valley Biomedical Cat#HP1022HI Recombinant Human IL-2 Peprotech Cat#200-02 Lymphoprep density gradient medium STEMCELL Technologies Cat#07801 (Continued on next page) Cell 186, 3983–4002.e1–e13, August 31, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Human T-Expander CD3/CD28 Thermo Fisher Scientific Cat#11141D X-VIVO 15 Serum-free Hematopoietic Cell Medium Lonza Cat#BE02-053Q Dulbecco0s Modifi–d Eagle0s Medium – low glucose Sigma-Aldrich Cat#D5546 Eagle’s minimal essential Medium (EMEM) ATCC Cat#30-2003 Opti-MEM reduced serum medium Thermo Fisher Scientific Cat#31985070 PEG 8000 Sigma-Aldrich Cat#25322-68-3 PEG-it Virus Precipitation Solution System Biosciences Cat#LV825A-1 Salt active nuclease ArcticZymes Cat#70910-202 0.9% NaCl Fresenius Kabi Cat#918610 BSA NEB Cat#B9000S Vybrant DyeCycle Ruby Thermo Fisher Cat#V10309 EZ-PREP buffer Sigma-Aldrich #NUC-101 Critical commercial assays Phusion U Multiplex PCR Master Mix Thermo Fisher Scientific Cat#F562L Q5 High-Fidelity 2 x Master Mix New England BioLabs Cat#M0492L Phusion Green Hot Start II High-Fidelity DNA Polymerase Thermo Fisher Scientific Cat#F537L QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 QIAGEN Plasmid Plus Midi Kit QIAGEN Cat#12943 QIAprep Spin Miniprep Kit QIAGEN Cat#27106 Qiagen Plasmid Plus 96 Miniprep Kit QIAGEN Cat#16181 EasySep Human T cell Isolation Kit STEMCELL Technologies Cat#17951 Neon Transfection System Thermo Fisher Scientific Cat#MPK1096 QuickExtract DNA Extraction Solution Lucigen Cat# QE09050 SE Cell Line 4DNucleofector X Kit S Lonza Cat#V4XC-1032 Illustra TempliPhi 100 amplification kit Cytiva Cat#25640010 NEB T7 HiScribe Kit New England BioLabs Cat#E2040S AAVpro Titration Kit version 2 Clontech/Takara Cat#6233 Agencourt DNAdvance Kit Beckman Coulter Cat#V10309 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 MiSeq Reagent Micro Kit v2 (300-cycles) Illumina Cat#MS-103-1002 (Continued on next page) ll OPEN ACCESS e2 Cell 186, 3983–4002.e1–e13, August 31, 2023 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Amplicon sequencing data This paper NCBI SRA: BioProject PRJNA916060 Experimental models: Cell lines Human (female): HEK293T ATCC Cat#CRL-3216 Mouse (male): N2a ATCC Cat#CCL-131 Human (female): HEK293T clone 17 ATCC Cat#CRL-11268 Primary human fibroblast (HEXA) Coriell Institute Cat#GM00221 Primary human fibroblast (UGT1A1) Coriell Institute Cat# GM09551 Primary human fibroblast (RECQL3) Coriell Institute Cat# GM02085 Primary human fibroblast (GAA) Coriell Institute Cat# GM20092 Experimental models: Organisms/strains Timed pregnant C57BL/6J mice Charles River Laboratories Cat#027 Oligonucleotides HEXA, 1278ins TATC pegRNA: mA*mU*mC*rCr UrUrCrCrArGrUrCrArGrGrGrCrCrArUrGrUrUrU rUrArGrArGrCrUrArGrArArArUrArGrCrArArGrUrU rArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCrArCr CrGrArGrUrCrGrGrUrGrCrGrUrArCrCrUrGrArAr CrCrGrUrArUrArUrCrGrUrArUrGrGrCrCrCrUrGr ArCrUrUrCrUrCrUrCrUrCrCrGrCrGrGrUrUrCr UrArUrCrUrArGrUrUrArCrGrCrGrUrUrAr ArArCrCrArArCrUrA*mG*mA*mA Integrated DNA Technologies N/A VEGFA, +2 G to A pegRNA: mG*mA*mU*rGrUr CrUrGrCrArGrGrCrCrArGrArUrGrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGr UrUrArArArArUrArArGrGrCrUrArGrUrCrCr GrUrUrArUrCrArArCrUrUrGrArArArArArGrUrGr GrCrArCrCrGrArGrUrCrGrGrUrGrCrArArUrGrUr GrCrCrArUrCrUrGrGrArGrCrArCrUrCrArUrCrUr GrGrCrCrUrGrCrArGrArArCrArArUrCrUrCrCrGr CrGrGrUrUrCrUrArUrCrUrArGrUrUrArCrGrCr GrUrUrArArArCrCrArArCrUrArGrArA*mU*mU*mU Integrated DNA Technologies N/A DNMT1, 1–15 deletion pegRNA: mG*mA*mU*rUr CrCrUrGrGrUrGrCrCrArGrArArArCrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGrUr UrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCr ArCrCrGrArGrUrCrGrGrUrGrCrArGrGrAr GrGrArArGrCrUrGrCrUrArArGrGrArCrUrArGrUrUr CrUrGrCrCrCrUrUrCrUrGrGrCrArCrCrArGrGrAr CrCrUrCrUrUrCrUrCrGrCrGrGrUrUrCrUrArUr CrUrArGrUrUrArCrGrCrGrUrUrArArArCrCrArArCrUr ArGrArA*mU*mU*mU Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Cell 186, 3983–4002.e1–e13, August 31, 2023 e3 Resource
Titration:Article Title: Phage-assisted evolution and protein engineering yield compact, efficient prime editors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains One Shot Mach1 T1 Phage-Resistant Chemically Competent E. coli Thermo Fisher Scientific Cat#C862003 E. coli S2060 Addgene #105064 Chemicals, peptides, and recombinant proteins BsaI-HFv2 New England BioLabs Cat#R3733S LguI (SapI) Thermo Fisher Scientific Cat#ER1932 T4 DNA Ligase New England BioLabs Cat#M0202S NEBuilder HiFi DNA assembly master mix New England BioLabs Cat#E2621S Dimethyl sulfoxide Sigma-Aldrich Cat#D8418-50ML Poly(ethylene glycol) 3350 Sigma-Aldrich Cat#P4338-500G DNaseI (Rnase-free) New England BioLabs Cat#M0303 Magnesium chloride solution Sigma-Aldrich Cat#M1028-10X1ML Carbenicillin Gold Biotechnology Cat#C-103 Chloramphenicol Gold Biotechnology Cat#C-105 Tetracycline Gold Biotechnology Cat#T-101 Streptomycin Gold Biotechnology Cat#S-150 L-arabinose Gold Biotechnology Cat#A-300 Glucose Sigma-Aldrich Cat#G7021 Bluo-gal Gold Biotechnology Cat#B-673-10 dNTPs New England BioLabs Cat#N0447S Lipofectamine 2000 Thermo Fisher Scientific Cat#11668019 TrypLE Thermo Fisher Scientific Cat#12605010 Proteinase K, recombinant, PCR grade Thermo Fisher Scientific Cat#11668019 SDS (10% wt/vol) Thermo Fisher Scientific Cat#15553027 DNAdvance Kit Beckman Coulter Cat#A48705 AMPure XP Beckman Coulter Cat#B23318 CleanCap Reagent AG TriLink BioTechnologies Cat#N-7113 N1 -Methylpseudouridine50 -Triphosphate TriLink BioTechnologies Cat#N-1081 LiCl Precipitation Solution (7.5 M) Thermo Fisher Scientific Cat#AM9480 DMEM, high glucose, GlutaMAX supplement Thermo Fisher Scientific Cat#10566016 Fetal bovine serum Thermo Fisher Scientific Cat#16000044 L-Glutamine Corning Cat#25-005-Cl Penicillin-Streptomycin Thermo Fisher Scientific Cat#15070063 GlutaMAX supplement Thermo Fisher Scientific Cat#35050061 N-acetyl-L-cysteine Sigma-Aldrich Cat#A7250-100G Human AB Serum Valley Biomedical Cat#HP1022HI Recombinant Human IL-2 Peprotech Cat#200-02 Lymphoprep density gradient medium STEMCELL Technologies Cat#07801 (Continued on next page) Cell 186, 3983–4002.e1–e13, August 31, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads Human T-Expander CD3/CD28 Thermo Fisher Scientific Cat#11141D X-VIVO 15 Serum-free Hematopoietic Cell Medium Lonza Cat#BE02-053Q Dulbecco0s Modifi–d Eagle0s Medium – low glucose Sigma-Aldrich Cat#D5546 Eagle’s minimal essential Medium (EMEM) ATCC Cat#30-2003 Opti-MEM reduced serum medium Thermo Fisher Scientific Cat#31985070 PEG 8000 Sigma-Aldrich Cat#25322-68-3 PEG-it Virus Precipitation Solution System Biosciences Cat#LV825A-1 Salt active nuclease ArcticZymes Cat#70910-202 0.9% NaCl Fresenius Kabi Cat#918610 BSA NEB Cat#B9000S Vybrant DyeCycle Ruby Thermo Fisher Cat#V10309 EZ-PREP buffer Sigma-Aldrich #NUC-101 Critical commercial assays Phusion U Multiplex PCR Master Mix Thermo Fisher Scientific Cat#F562L Q5 High-Fidelity 2 x Master Mix New England BioLabs Cat#M0492L Phusion Green Hot Start II High-Fidelity DNA Polymerase Thermo Fisher Scientific Cat#F537L QIAquick PCR Purification Kit QIAGEN Cat#28104 QIAquick Gel Extraction Kit QIAGEN Cat#28704 QIAGEN Plasmid Plus Midi Kit QIAGEN Cat#12943 QIAprep Spin Miniprep Kit QIAGEN Cat#27106 Qiagen Plasmid Plus 96 Miniprep Kit QIAGEN Cat#16181 EasySep Human T cell Isolation Kit STEMCELL Technologies Cat#17951 Neon Transfection System Thermo Fisher Scientific Cat#MPK1096 QuickExtract DNA Extraction Solution Lucigen Cat# QE09050 SE Cell Line 4DNucleofector X Kit S Lonza Cat#V4XC-1032 Illustra TempliPhi 100 amplification kit Cytiva Cat#25640010 NEB T7 HiScribe Kit New England BioLabs Cat#E2040S AAVpro Titration Kit version 2 Clontech/Takara Cat#6233 Agencourt DNAdvance Kit Beckman Coulter Cat#V10309 MiSeq Reagent Kit v2 (300-cycles) Illumina Cat#MS-102-2002 MiSeq Reagent Micro Kit v2 (300-cycles) Illumina Cat#MS-103-1002 (Continued on next page) ll OPEN ACCESS e2 Cell 186, 3983–4002.e1–e13, August 31, 2023 Resource .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Amplicon sequencing data This paper NCBI SRA: BioProject PRJNA916060 Experimental models: Cell lines Human (female): HEK293T ATCC Cat#CRL-3216 Mouse (male): N2a ATCC Cat#CCL-131 Human (female): HEK293T clone 17 ATCC Cat#CRL-11268 Primary human fibroblast (HEXA) Coriell Institute Cat#GM00221 Primary human fibroblast (UGT1A1) Coriell Institute Cat# GM09551 Primary human fibroblast (RECQL3) Coriell Institute Cat# GM02085 Primary human fibroblast (GAA) Coriell Institute Cat# GM20092 Experimental models: Organisms/strains Timed pregnant C57BL/6J mice Charles River Laboratories Cat#027 Oligonucleotides HEXA, 1278ins TATC pegRNA: mA*mU*mC*rCr UrUrCrCrArGrUrCrArGrGrGrCrCrArUrGrUrUrU rUrArGrArGrCrUrArGrArArArUrArGrCrArArGrUrU rArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCrArCr CrGrArGrUrCrGrGrUrGrCrGrUrArCrCrUrGrArAr CrCrGrUrArUrArUrCrGrUrArUrGrGrCrCrCrUrGr ArCrUrUrCrUrCrUrCrUrCrCrGrCrGrGrUrUrCr UrArUrCrUrArGrUrUrArCrGrCrGrUrUrAr ArArCrCrArArCrUrA*mG*mA*mA Integrated DNA Technologies N/A VEGFA, +2 G to A pegRNA: mG*mA*mU*rGrUr CrUrGrCrArGrGrCrCrArGrArUrGrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGr UrUrArArArArUrArArGrGrCrUrArGrUrCrCr GrUrUrArUrCrArArCrUrUrGrArArArArArGrUrGr GrCrArCrCrGrArGrUrCrGrGrUrGrCrArArUrGrUr GrCrCrArUrCrUrGrGrArGrCrArCrUrCrArUrCrUr GrGrCrCrUrGrCrArGrArArCrArArUrCrUrCrCrGr CrGrGrUrUrCrUrArUrCrUrArGrUrUrArCrGrCr GrUrUrArArArCrCrArArCrUrArGrArA*mU*mU*mU Integrated DNA Technologies N/A DNMT1, 1–15 deletion pegRNA: mG*mA*mU*rUr CrCrUrGrGrUrGrCrCrArGrArArArCrArGrUrUrUr UrArGrArGrCrUrArGrArArArUrArGrCrArArGrUr UrArArArArUrArArGrGrCrUrArGrUrCrCrGrUrUrAr UrCrArArCrUrUrGrArArArArArGrUrGrGrCr ArCrCrGrArGrUrCrGrGrUrGrCrArGrGrAr GrGrArArGrCrUrGrCrUrArArGrGrArCrUrArGrUrUr CrUrGrCrCrCrUrUrCrUrGrGrCrArCrCrArGrGrAr CrCrUrCrUrUrCrUrCrGrCrGrGrUrUrCrUrArUr CrUrArGrUrUrArCrGrCrGrUrUrArArArCrCrArArCrUr ArGrArA*mU*mU*mU Integrated DNA Technologies N/A (Continued on next page) ll OPEN ACCESS Cell 186, 3983–4002.e1–e13, August 31, 2023 e3 Resource
|
ATCC is a verified supplier 
ATCC manufactures this product 