Recombinant:Article Title: Knockout of the LRRK2-counteracting RAB phosphatase PPM1H disrupts axonal autophagy and exacerbates alpha-synuclein aggregation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-RAB10 antibody, Mouse Monoclonal Nanotools 0680-100/Rab10-605B11; RRID: AB_2921226 Anti-RAB10 (phospho T73) antibody, Rabbit Monoclonal Abcam ab230261; RRID: AB_2811274 Anti-RAB12 antibody, Mouse Monoclonal Santa Cruz Biotechnology sc-515613; RRID: AB_3101762 Anti-RAB12 (phospho S106), Rabbit Monoclonal Abcam ab256487; RRID: AB_2884880 Anti-PPM1H antibody, Sheep Polyclonal MRC PPU reagents and services, University of Dundee, Scotland DA018, 3rd bleed; RRID: AB_2923281 Anti-LRRK2 antibody, Rabbit Monoclonal Abcam ab133474; RRID: AB_2713963 Anti-αSynuclein antibody, Rabbit Monoclonal Cell Signaling 4179; RRID: AB_1904156 Anti-Rabbit IgG-IRDye 800CW, Donkey Polyclonal Li-COR Biosciences 926-32213; RRID: AB_621848 Anti-Mouse IgG-IRDye 680RD, Donkey Polyclonal Li-COR Biosciences 926-68073; RRID: AB_10954442 Anti-Sheep Alexa Fluor 680, Donkey Polyclonal Thermo Fisher A21102; RRID: AB_10374469 Anti-αSynuclein (phospho S129) antibody, Rabbit Monoclonal Abcam ab51253; RRID: AB_869973 Anti-αSynuclein (phospho S129) antibody, Mouse Monoclonal BioLegend 825701; RRID: AB_2564891 Anti-LC3 antibody, Rabbit Polyclonal Abcam ab48394; RRID: AB_881433 Anti-GABARAP/L1/L2 antibody, Rabbit Monoclonal Abcam ab109364; RRID: AB_10861928 Anti-αSynuclein antibody, Mouse Monoclonal BD 610787; RRID: AB_398108 Anti-Synapsin1/2 antibody, Rabbit Polyclonal Synaptic Systems 106002; RRID: AB_887804 Anti-Bassoon antibody, Guinea Pig Monoclonal Synaptic Systems 141318; RRID: AB_2927388 Anti-Homer1 antibody, Rabbit Polyclonal Synaptic Systems 160003; RRID: AB_887730 Anti-MAP2 antibody, Mouse Monoclonal Millipore MAB3418; RRID: AB_94856 Anti-MAP2 antibody, Chicken Polyclonal Abcam ab5392; RRID: AB_2138153 Anti-Chicken Alexa Fluor 405, Goat Polyclonal Thermo Fisher A-48260; RRID: AB_2890271 Anti-Rabbit Alexa Fluor 488, Goat Polyclonal Thermo Fisher A-11034; RRID: AB_2576217 Anti-Mouse Alexa Fluor 488, Goat Polyclonal Thermo Fisher A-11001; RRID: AB_2534069 Anti-Mouse Alexa Fluor 594, Goat Polyclonal Thermo Fisher A-11005; RRID: AB_2534073 (Continued on next page) 14 Cell Reports 45, 117364, June 23, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Mouse Alexa Fluor 546, Goat Polyclonal Thermo Fisher A-11030; RRID: AB_2737024 Anti-Chicken Alexa Fluor 647, Goat Polyclonal Thermo Fisher A-21449; RRID: AB_2535866 Anti-Rabbit Alexa Fluor 647, Goat Polyclonal Thermo Fisher A-21245; RRID: AB_2535813 Chemicals, peptides, and recombinant proteins MLi-2 Tocris 5756 DMSO AppliChem A3672,0100 Poly-L-Lysine (mol wt 70,000–150,000) Sigma-Aldrich P1274 HBSS (10x) Thermo Fisher 14185–052 1M HEPES Thermo Fisher 15630–080 2.5% Trypsin Thermo Fisher 15090–046 Minimum essential medium (MEM) Thermo Fisher 11095–072 Horse serum (heat inactivated) Thermo Fisher 16050–122 Sodium pyruvate Thermo Fisher 11360–039 D-Glucose solution 45% Sigma-Aldrich G8769 GlutaMAX Thermo Fisher 35050061 B27 Supplement Thermo Fisher 17504–044 Neurobasal Medium Thermo Fisher 21103–049 Penicillin-Streptomycin Thermo Fisher 15140–122 Lipofectamine 2000 Transfection Reagent Thermo Fisher 11668019 Matrigel Growth Factor Reduced Corning 354230 Essential 8 Medium Thermo Fisher A1517001 ReLeSR Stemcell Technologies 05872 Accutase Sigma-Aldrich A6964 ROCK Inhibitor Y-27632 Selleckchem S1049 Knockout Serum Replacement Thermo Fisher 10828010 DMEM/F-12, HEPES Thermo Fisher 11330032 N2 Supplement Thermo Fisher 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher 11140050 Doxycycline Sigma-Aldrich D9891 Poly-L-Ornithine Sigma-Aldrich P3655 BrainPhys Neuronal Medium Stemcell Technologies 05790 Lipofectamine STEM Transfection Reagent Thermo Fisher STEM00003 Laminin Corning 354232 BDNF PeproTech 450–02 NT-3 PeproTech 450–03 Microcystin-LR Sigma-Aldrich 475815 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher 78442 Pepstatin A Sigma-Aldrich P5318 E64d Sigma-Aldrich E8640 5-Fluoro-2′-deoxyuridine Sigma-Aldrich F0503 Uridine Sigma-Aldrich U3003 EveryBlot Blocking Buffer BioRad 12010020 Critical commercial assays BCA Protein Assay Kit Thermo Fisher 23225 ZymoPURE II Plasmid Maxiprep Kit ZymoResearch D4203 (Continued on next page) Cell Reports 45, 117364, June 23, 2026 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: cell lines Human: KOLF2.1J WT iPSCs B. Skarnes (Jackson Laboratories, Connecticut) RRID: CVCL_B5P3 Human: KOLF2.1J LRRK2-R1441H iPSCs B. Skarnes (Jackson Laboratories, Connecticut) N/A Human: KOLF2.1J PPM1H KO iPSCs Dou et al.13 RRID: CVCL_C7TY Experimental models: organisms/strains Mouse: LRRK2-G2019S knock-in Taconic 13940 Mouse: C57BL/6NTac WT Taconic B6 Mouse: PPM1H knock-out Taconic TF3142 Recombinant DNA Plasmid: CMV mScarlet-LC3B Modified from EGFP-LC3B (gift from T. Yoshimori, Osaka University, Japan) Addgene plasmid #200431 Plasmid: PGK mCherry-LC3B Modified from pLEX PGK mCherry-LC3B (gift from Michael Ward, NIH) N/A Plasmid: CMV SEP-LAMP1-RFP Gift from J. Bonifacino (NIH) Addgene plasmid #167970 Plasmid: CMV aSyn-EGFP VectorBuilder, same linker as described in56 VB230227-1242vtx Plasmid: PGK aSyn-EGFP VectorBuilder, same linker as described in56 VB251105-1468fsr Plasmid: PB-TO-hNGN2 Gift from iPSC Neurodegenerative Disease Initiative (iNDI) & Michael Ward Addgene plasmid #172115 Plasmid: piggyBacTM transposase vector Transposagen N/A Software and algorithms FIJI (Release 2.9.0) NIH, USA http://fiji.sc Prism 10 GraphPad https://www.graphpad.com/ scientific-software/prism/ RStudio: Integrated Development for R (2022.07.0) RStudio Team http://www.rstudio.com/ R package: nlme Pinheiro J, Bates D, R Core Team http://CRAN.R-project.org/package=nlme R package: lme4 Bates D, Mächler M, Bolker B, Walker S https://cran.r-project.org/web/ packages/lme4/index.html MATLAB R2022a MathWorks https://www.mathworks.com/ products/matlab.html KymoSuite (custom MATLAB script) Guedes-Dias et al.57 https://github.com/jnirschl/kinesin- 3_guedes-dias_2018/tree/master/kymoSuite, https://zenodo.org/record/2530934 VisiView Visitron https://www.visitron.de/products/ visiviewr-software.html ZEN blue Zeiss https://www.zeiss.com/microscopy/ en/products/software/zeiss-zen.html Image Studio LI-COR https://www.licor.com/bio/image-studio/ Adobe Illustrator 2023 Adobe https://www.adobe.com/ products/illustrator.html BioRender BioRender https://biorender.com/ Other 35 mm #1.5 glass bottom imaging dishes MatTek P35G-1.5-20-C 12 mm #1.5 glass coverslips R. Langenbrinck GmbH 01-0012/5 ProLong Gold Antifade Mountant Thermo Fisher P36930 16 Cell Reports 45, 117364, June 23, 2026
Article Title: Protocol for antibody-dependent cellular phagocytosis assay with controlled IgG concentrations in tested samples.
Article Snippet: .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Anti-human IgG Fab-specific, 1 mg/mL SouthernBiotech 2085-01 Biological samples Serum from vaccinated seropositive individuals FHCC IRB#10453 Serum from Seattle-area seroepidemiology study participants University of Washington NCT04338360 Pooled anti-SARS-CoV-2 serum University of Washington NCT04344977 Chemicals, peptides, and recombinant proteins RPMI 1640 Gibco 11875-093 Sodium pyruvate Gibco 11360-070 Sodium bicarbonate Gibco 25080-094 HEPES Gibco 15630-080 PenStrep Gibco 15070-063 Fetal bovine serum (FBS) HyClone SH30071.03 Phosphate-buffered solution (PBS) Gibco 14190-144 Tween-20 Sigma-Aldrich P7949-500ML Sodium Azide Millipore Sigma S8032 Paraformaldehyde Boster AR1068 Sulfo-NHS-LC-biotin Thermo Scientific A39257 Sulfo-NHS Thermo Scientific A39269 EDC Thermo Scientific 77149 Trypan Blue stain Invitrogen T10282 Experimental models: Cell lines THP-1 monocytes ATCC TIB-202 Software and algorithms GraphPad Prism GraphPad Software https://www.graphpad.com/how-to-buy/ FlowJo BD Biosciences https://www.flowjo.com/flowjo/download Bio-Plex Manager Bio-Rad https://www.bio-rad.com/en-us/product/ bio-plex-manager-software-standard- edition?ID=5846e84e-03a7-4599a8ae-7ba5dd2c7684 Other Zeba spin desalting column Thermo Scientific 89882 Bio-Plex ProTM Flat Bottom Plates Bio-Rad 171025001 Blotting-grade blocker Bio-Rad 1706404 Tissue Culture Plates, 96-well, U-bottom Genesee Scientific 25-221 NeutrAvidin-labeled microspheres Invitrogen F8776 Bovine serum albumin SAFC Biosciences B4287-100G Bio-Plex Pro Magnetic COOH beads Bio-Rad MC10027-01 Bio-Plex 200 System Bio-Rad N/A BCP Wash buffer Reagent Final concentration Amount Tween-20 (25%) 0.05% 0.4 mL NaN 3 (10%) 0.1% 2 mL Bovine serum albumin 10 mg/mL 2 g PBS N/A 195.6 mL Total N/A 200 mL [Store at room temperature, maximum storage time of 1 month or prepare fresh per experiment]. ..
Transfection:Article Title: Knockout of the LRRK2-counteracting RAB phosphatase PPM1H disrupts axonal autophagy and exacerbates alpha-synuclein aggregation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-RAB10 antibody, Mouse Monoclonal Nanotools 0680-100/Rab10-605B11; RRID: AB_2921226 Anti-RAB10 (phospho T73) antibody, Rabbit Monoclonal Abcam ab230261; RRID: AB_2811274 Anti-RAB12 antibody, Mouse Monoclonal Santa Cruz Biotechnology sc-515613; RRID: AB_3101762 Anti-RAB12 (phospho S106), Rabbit Monoclonal Abcam ab256487; RRID: AB_2884880 Anti-PPM1H antibody, Sheep Polyclonal MRC PPU reagents and services, University of Dundee, Scotland DA018, 3rd bleed; RRID: AB_2923281 Anti-LRRK2 antibody, Rabbit Monoclonal Abcam ab133474; RRID: AB_2713963 Anti-αSynuclein antibody, Rabbit Monoclonal Cell Signaling 4179; RRID: AB_1904156 Anti-Rabbit IgG-IRDye 800CW, Donkey Polyclonal Li-COR Biosciences 926-32213; RRID: AB_621848 Anti-Mouse IgG-IRDye 680RD, Donkey Polyclonal Li-COR Biosciences 926-68073; RRID: AB_10954442 Anti-Sheep Alexa Fluor 680, Donkey Polyclonal Thermo Fisher A21102; RRID: AB_10374469 Anti-αSynuclein (phospho S129) antibody, Rabbit Monoclonal Abcam ab51253; RRID: AB_869973 Anti-αSynuclein (phospho S129) antibody, Mouse Monoclonal BioLegend 825701; RRID: AB_2564891 Anti-LC3 antibody, Rabbit Polyclonal Abcam ab48394; RRID: AB_881433 Anti-GABARAP/L1/L2 antibody, Rabbit Monoclonal Abcam ab109364; RRID: AB_10861928 Anti-αSynuclein antibody, Mouse Monoclonal BD 610787; RRID: AB_398108 Anti-Synapsin1/2 antibody, Rabbit Polyclonal Synaptic Systems 106002; RRID: AB_887804 Anti-Bassoon antibody, Guinea Pig Monoclonal Synaptic Systems 141318; RRID: AB_2927388 Anti-Homer1 antibody, Rabbit Polyclonal Synaptic Systems 160003; RRID: AB_887730 Anti-MAP2 antibody, Mouse Monoclonal Millipore MAB3418; RRID: AB_94856 Anti-MAP2 antibody, Chicken Polyclonal Abcam ab5392; RRID: AB_2138153 Anti-Chicken Alexa Fluor 405, Goat Polyclonal Thermo Fisher A-48260; RRID: AB_2890271 Anti-Rabbit Alexa Fluor 488, Goat Polyclonal Thermo Fisher A-11034; RRID: AB_2576217 Anti-Mouse Alexa Fluor 488, Goat Polyclonal Thermo Fisher A-11001; RRID: AB_2534069 Anti-Mouse Alexa Fluor 594, Goat Polyclonal Thermo Fisher A-11005; RRID: AB_2534073 (Continued on next page) 14 Cell Reports 45, 117364, June 23, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Mouse Alexa Fluor 546, Goat Polyclonal Thermo Fisher A-11030; RRID: AB_2737024 Anti-Chicken Alexa Fluor 647, Goat Polyclonal Thermo Fisher A-21449; RRID: AB_2535866 Anti-Rabbit Alexa Fluor 647, Goat Polyclonal Thermo Fisher A-21245; RRID: AB_2535813 Chemicals, peptides, and recombinant proteins MLi-2 Tocris 5756 DMSO AppliChem A3672,0100 Poly-L-Lysine (mol wt 70,000–150,000) Sigma-Aldrich P1274 HBSS (10x) Thermo Fisher 14185–052 1M HEPES Thermo Fisher 15630–080 2.5% Trypsin Thermo Fisher 15090–046 Minimum essential medium (MEM) Thermo Fisher 11095–072 Horse serum (heat inactivated) Thermo Fisher 16050–122 Sodium pyruvate Thermo Fisher 11360–039 D-Glucose solution 45% Sigma-Aldrich G8769 GlutaMAX Thermo Fisher 35050061 B27 Supplement Thermo Fisher 17504–044 Neurobasal Medium Thermo Fisher 21103–049 Penicillin-Streptomycin Thermo Fisher 15140–122 Lipofectamine 2000 Transfection Reagent Thermo Fisher 11668019 Matrigel Growth Factor Reduced Corning 354230 Essential 8 Medium Thermo Fisher A1517001 ReLeSR Stemcell Technologies 05872 Accutase Sigma-Aldrich A6964 ROCK Inhibitor Y-27632 Selleckchem S1049 Knockout Serum Replacement Thermo Fisher 10828010 DMEM/F-12, HEPES Thermo Fisher 11330032 N2 Supplement Thermo Fisher 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher 11140050 Doxycycline Sigma-Aldrich D9891 Poly-L-Ornithine Sigma-Aldrich P3655 BrainPhys Neuronal Medium Stemcell Technologies 05790 Lipofectamine STEM Transfection Reagent Thermo Fisher STEM00003 Laminin Corning 354232 BDNF PeproTech 450–02 NT-3 PeproTech 450–03 Microcystin-LR Sigma-Aldrich 475815 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher 78442 Pepstatin A Sigma-Aldrich P5318 E64d Sigma-Aldrich E8640 5-Fluoro-2′-deoxyuridine Sigma-Aldrich F0503 Uridine Sigma-Aldrich U3003 EveryBlot Blocking Buffer BioRad 12010020 Critical commercial assays BCA Protein Assay Kit Thermo Fisher 23225 ZymoPURE II Plasmid Maxiprep Kit ZymoResearch D4203 (Continued on next page) Cell Reports 45, 117364, June 23, 2026 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: cell lines Human: KOLF2.1J WT iPSCs B. Skarnes (Jackson Laboratories, Connecticut) RRID: CVCL_B5P3 Human: KOLF2.1J LRRK2-R1441H iPSCs B. Skarnes (Jackson Laboratories, Connecticut) N/A Human: KOLF2.1J PPM1H KO iPSCs Dou et al.13 RRID: CVCL_C7TY Experimental models: organisms/strains Mouse: LRRK2-G2019S knock-in Taconic 13940 Mouse: C57BL/6NTac WT Taconic B6 Mouse: PPM1H knock-out Taconic TF3142 Recombinant DNA Plasmid: CMV mScarlet-LC3B Modified from EGFP-LC3B (gift from T. Yoshimori, Osaka University, Japan) Addgene plasmid #200431 Plasmid: PGK mCherry-LC3B Modified from pLEX PGK mCherry-LC3B (gift from Michael Ward, NIH) N/A Plasmid: CMV SEP-LAMP1-RFP Gift from J. Bonifacino (NIH) Addgene plasmid #167970 Plasmid: CMV aSyn-EGFP VectorBuilder, same linker as described in56 VB230227-1242vtx Plasmid: PGK aSyn-EGFP VectorBuilder, same linker as described in56 VB251105-1468fsr Plasmid: PB-TO-hNGN2 Gift from iPSC Neurodegenerative Disease Initiative (iNDI) & Michael Ward Addgene plasmid #172115 Plasmid: piggyBacTM transposase vector Transposagen N/A Software and algorithms FIJI (Release 2.9.0) NIH, USA http://fiji.sc Prism 10 GraphPad https://www.graphpad.com/ scientific-software/prism/ RStudio: Integrated Development for R (2022.07.0) RStudio Team http://www.rstudio.com/ R package: nlme Pinheiro J, Bates D, R Core Team http://CRAN.R-project.org/package=nlme R package: lme4 Bates D, Mächler M, Bolker B, Walker S https://cran.r-project.org/web/ packages/lme4/index.html MATLAB R2022a MathWorks https://www.mathworks.com/ products/matlab.html KymoSuite (custom MATLAB script) Guedes-Dias et al.57 https://github.com/jnirschl/kinesin- 3_guedes-dias_2018/tree/master/kymoSuite, https://zenodo.org/record/2530934 VisiView Visitron https://www.visitron.de/products/ visiviewr-software.html ZEN blue Zeiss https://www.zeiss.com/microscopy/ en/products/software/zeiss-zen.html Image Studio LI-COR https://www.licor.com/bio/image-studio/ Adobe Illustrator 2023 Adobe https://www.adobe.com/ products/illustrator.html BioRender BioRender https://biorender.com/ Other 35 mm #1.5 glass bottom imaging dishes MatTek P35G-1.5-20-C 12 mm #1.5 glass coverslips R. Langenbrinck GmbH 01-0012/5 ProLong Gold Antifade Mountant Thermo Fisher P36930 16 Cell Reports 45, 117364, June 23, 2026
Knock-Out:Article Title: Knockout of the LRRK2-counteracting RAB phosphatase PPM1H disrupts axonal autophagy and exacerbates alpha-synuclein aggregation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-RAB10 antibody, Mouse Monoclonal Nanotools 0680-100/Rab10-605B11; RRID: AB_2921226 Anti-RAB10 (phospho T73) antibody, Rabbit Monoclonal Abcam ab230261; RRID: AB_2811274 Anti-RAB12 antibody, Mouse Monoclonal Santa Cruz Biotechnology sc-515613; RRID: AB_3101762 Anti-RAB12 (phospho S106), Rabbit Monoclonal Abcam ab256487; RRID: AB_2884880 Anti-PPM1H antibody, Sheep Polyclonal MRC PPU reagents and services, University of Dundee, Scotland DA018, 3rd bleed; RRID: AB_2923281 Anti-LRRK2 antibody, Rabbit Monoclonal Abcam ab133474; RRID: AB_2713963 Anti-αSynuclein antibody, Rabbit Monoclonal Cell Signaling 4179; RRID: AB_1904156 Anti-Rabbit IgG-IRDye 800CW, Donkey Polyclonal Li-COR Biosciences 926-32213; RRID: AB_621848 Anti-Mouse IgG-IRDye 680RD, Donkey Polyclonal Li-COR Biosciences 926-68073; RRID: AB_10954442 Anti-Sheep Alexa Fluor 680, Donkey Polyclonal Thermo Fisher A21102; RRID: AB_10374469 Anti-αSynuclein (phospho S129) antibody, Rabbit Monoclonal Abcam ab51253; RRID: AB_869973 Anti-αSynuclein (phospho S129) antibody, Mouse Monoclonal BioLegend 825701; RRID: AB_2564891 Anti-LC3 antibody, Rabbit Polyclonal Abcam ab48394; RRID: AB_881433 Anti-GABARAP/L1/L2 antibody, Rabbit Monoclonal Abcam ab109364; RRID: AB_10861928 Anti-αSynuclein antibody, Mouse Monoclonal BD 610787; RRID: AB_398108 Anti-Synapsin1/2 antibody, Rabbit Polyclonal Synaptic Systems 106002; RRID: AB_887804 Anti-Bassoon antibody, Guinea Pig Monoclonal Synaptic Systems 141318; RRID: AB_2927388 Anti-Homer1 antibody, Rabbit Polyclonal Synaptic Systems 160003; RRID: AB_887730 Anti-MAP2 antibody, Mouse Monoclonal Millipore MAB3418; RRID: AB_94856 Anti-MAP2 antibody, Chicken Polyclonal Abcam ab5392; RRID: AB_2138153 Anti-Chicken Alexa Fluor 405, Goat Polyclonal Thermo Fisher A-48260; RRID: AB_2890271 Anti-Rabbit Alexa Fluor 488, Goat Polyclonal Thermo Fisher A-11034; RRID: AB_2576217 Anti-Mouse Alexa Fluor 488, Goat Polyclonal Thermo Fisher A-11001; RRID: AB_2534069 Anti-Mouse Alexa Fluor 594, Goat Polyclonal Thermo Fisher A-11005; RRID: AB_2534073 (Continued on next page) 14 Cell Reports 45, 117364, June 23, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Mouse Alexa Fluor 546, Goat Polyclonal Thermo Fisher A-11030; RRID: AB_2737024 Anti-Chicken Alexa Fluor 647, Goat Polyclonal Thermo Fisher A-21449; RRID: AB_2535866 Anti-Rabbit Alexa Fluor 647, Goat Polyclonal Thermo Fisher A-21245; RRID: AB_2535813 Chemicals, peptides, and recombinant proteins MLi-2 Tocris 5756 DMSO AppliChem A3672,0100 Poly-L-Lysine (mol wt 70,000–150,000) Sigma-Aldrich P1274 HBSS (10x) Thermo Fisher 14185–052 1M HEPES Thermo Fisher 15630–080 2.5% Trypsin Thermo Fisher 15090–046 Minimum essential medium (MEM) Thermo Fisher 11095–072 Horse serum (heat inactivated) Thermo Fisher 16050–122 Sodium pyruvate Thermo Fisher 11360–039 D-Glucose solution 45% Sigma-Aldrich G8769 GlutaMAX Thermo Fisher 35050061 B27 Supplement Thermo Fisher 17504–044 Neurobasal Medium Thermo Fisher 21103–049 Penicillin-Streptomycin Thermo Fisher 15140–122 Lipofectamine 2000 Transfection Reagent Thermo Fisher 11668019 Matrigel Growth Factor Reduced Corning 354230 Essential 8 Medium Thermo Fisher A1517001 ReLeSR Stemcell Technologies 05872 Accutase Sigma-Aldrich A6964 ROCK Inhibitor Y-27632 Selleckchem S1049 Knockout Serum Replacement Thermo Fisher 10828010 DMEM/F-12, HEPES Thermo Fisher 11330032 N2 Supplement Thermo Fisher 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher 11140050 Doxycycline Sigma-Aldrich D9891 Poly-L-Ornithine Sigma-Aldrich P3655 BrainPhys Neuronal Medium Stemcell Technologies 05790 Lipofectamine STEM Transfection Reagent Thermo Fisher STEM00003 Laminin Corning 354232 BDNF PeproTech 450–02 NT-3 PeproTech 450–03 Microcystin-LR Sigma-Aldrich 475815 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher 78442 Pepstatin A Sigma-Aldrich P5318 E64d Sigma-Aldrich E8640 5-Fluoro-2′-deoxyuridine Sigma-Aldrich F0503 Uridine Sigma-Aldrich U3003 EveryBlot Blocking Buffer BioRad 12010020 Critical commercial assays BCA Protein Assay Kit Thermo Fisher 23225 ZymoPURE II Plasmid Maxiprep Kit ZymoResearch D4203 (Continued on next page) Cell Reports 45, 117364, June 23, 2026 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: cell lines Human: KOLF2.1J WT iPSCs B. Skarnes (Jackson Laboratories, Connecticut) RRID: CVCL_B5P3 Human: KOLF2.1J LRRK2-R1441H iPSCs B. Skarnes (Jackson Laboratories, Connecticut) N/A Human: KOLF2.1J PPM1H KO iPSCs Dou et al.13 RRID: CVCL_C7TY Experimental models: organisms/strains Mouse: LRRK2-G2019S knock-in Taconic 13940 Mouse: C57BL/6NTac WT Taconic B6 Mouse: PPM1H knock-out Taconic TF3142 Recombinant DNA Plasmid: CMV mScarlet-LC3B Modified from EGFP-LC3B (gift from T. Yoshimori, Osaka University, Japan) Addgene plasmid #200431 Plasmid: PGK mCherry-LC3B Modified from pLEX PGK mCherry-LC3B (gift from Michael Ward, NIH) N/A Plasmid: CMV SEP-LAMP1-RFP Gift from J. Bonifacino (NIH) Addgene plasmid #167970 Plasmid: CMV aSyn-EGFP VectorBuilder, same linker as described in56 VB230227-1242vtx Plasmid: PGK aSyn-EGFP VectorBuilder, same linker as described in56 VB251105-1468fsr Plasmid: PB-TO-hNGN2 Gift from iPSC Neurodegenerative Disease Initiative (iNDI) & Michael Ward Addgene plasmid #172115 Plasmid: piggyBacTM transposase vector Transposagen N/A Software and algorithms FIJI (Release 2.9.0) NIH, USA http://fiji.sc Prism 10 GraphPad https://www.graphpad.com/ scientific-software/prism/ RStudio: Integrated Development for R (2022.07.0) RStudio Team http://www.rstudio.com/ R package: nlme Pinheiro J, Bates D, R Core Team http://CRAN.R-project.org/package=nlme R package: lme4 Bates D, Mächler M, Bolker B, Walker S https://cran.r-project.org/web/ packages/lme4/index.html MATLAB R2022a MathWorks https://www.mathworks.com/ products/matlab.html KymoSuite (custom MATLAB script) Guedes-Dias et al.57 https://github.com/jnirschl/kinesin- 3_guedes-dias_2018/tree/master/kymoSuite, https://zenodo.org/record/2530934 VisiView Visitron https://www.visitron.de/products/ visiviewr-software.html ZEN blue Zeiss https://www.zeiss.com/microscopy/ en/products/software/zeiss-zen.html Image Studio LI-COR https://www.licor.com/bio/image-studio/ Adobe Illustrator 2023 Adobe https://www.adobe.com/ products/illustrator.html BioRender BioRender https://biorender.com/ Other 35 mm #1.5 glass bottom imaging dishes MatTek P35G-1.5-20-C 12 mm #1.5 glass coverslips R. Langenbrinck GmbH 01-0012/5 ProLong Gold Antifade Mountant Thermo Fisher P36930 16 Cell Reports 45, 117364, June 23, 2026
Blocking Assay:Article Title: Knockout of the LRRK2-counteracting RAB phosphatase PPM1H disrupts axonal autophagy and exacerbates alpha-synuclein aggregation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-RAB10 antibody, Mouse Monoclonal Nanotools 0680-100/Rab10-605B11; RRID: AB_2921226 Anti-RAB10 (phospho T73) antibody, Rabbit Monoclonal Abcam ab230261; RRID: AB_2811274 Anti-RAB12 antibody, Mouse Monoclonal Santa Cruz Biotechnology sc-515613; RRID: AB_3101762 Anti-RAB12 (phospho S106), Rabbit Monoclonal Abcam ab256487; RRID: AB_2884880 Anti-PPM1H antibody, Sheep Polyclonal MRC PPU reagents and services, University of Dundee, Scotland DA018, 3rd bleed; RRID: AB_2923281 Anti-LRRK2 antibody, Rabbit Monoclonal Abcam ab133474; RRID: AB_2713963 Anti-αSynuclein antibody, Rabbit Monoclonal Cell Signaling 4179; RRID: AB_1904156 Anti-Rabbit IgG-IRDye 800CW, Donkey Polyclonal Li-COR Biosciences 926-32213; RRID: AB_621848 Anti-Mouse IgG-IRDye 680RD, Donkey Polyclonal Li-COR Biosciences 926-68073; RRID: AB_10954442 Anti-Sheep Alexa Fluor 680, Donkey Polyclonal Thermo Fisher A21102; RRID: AB_10374469 Anti-αSynuclein (phospho S129) antibody, Rabbit Monoclonal Abcam ab51253; RRID: AB_869973 Anti-αSynuclein (phospho S129) antibody, Mouse Monoclonal BioLegend 825701; RRID: AB_2564891 Anti-LC3 antibody, Rabbit Polyclonal Abcam ab48394; RRID: AB_881433 Anti-GABARAP/L1/L2 antibody, Rabbit Monoclonal Abcam ab109364; RRID: AB_10861928 Anti-αSynuclein antibody, Mouse Monoclonal BD 610787; RRID: AB_398108 Anti-Synapsin1/2 antibody, Rabbit Polyclonal Synaptic Systems 106002; RRID: AB_887804 Anti-Bassoon antibody, Guinea Pig Monoclonal Synaptic Systems 141318; RRID: AB_2927388 Anti-Homer1 antibody, Rabbit Polyclonal Synaptic Systems 160003; RRID: AB_887730 Anti-MAP2 antibody, Mouse Monoclonal Millipore MAB3418; RRID: AB_94856 Anti-MAP2 antibody, Chicken Polyclonal Abcam ab5392; RRID: AB_2138153 Anti-Chicken Alexa Fluor 405, Goat Polyclonal Thermo Fisher A-48260; RRID: AB_2890271 Anti-Rabbit Alexa Fluor 488, Goat Polyclonal Thermo Fisher A-11034; RRID: AB_2576217 Anti-Mouse Alexa Fluor 488, Goat Polyclonal Thermo Fisher A-11001; RRID: AB_2534069 Anti-Mouse Alexa Fluor 594, Goat Polyclonal Thermo Fisher A-11005; RRID: AB_2534073 (Continued on next page) 14 Cell Reports 45, 117364, June 23, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Mouse Alexa Fluor 546, Goat Polyclonal Thermo Fisher A-11030; RRID: AB_2737024 Anti-Chicken Alexa Fluor 647, Goat Polyclonal Thermo Fisher A-21449; RRID: AB_2535866 Anti-Rabbit Alexa Fluor 647, Goat Polyclonal Thermo Fisher A-21245; RRID: AB_2535813 Chemicals, peptides, and recombinant proteins MLi-2 Tocris 5756 DMSO AppliChem A3672,0100 Poly-L-Lysine (mol wt 70,000–150,000) Sigma-Aldrich P1274 HBSS (10x) Thermo Fisher 14185–052 1M HEPES Thermo Fisher 15630–080 2.5% Trypsin Thermo Fisher 15090–046 Minimum essential medium (MEM) Thermo Fisher 11095–072 Horse serum (heat inactivated) Thermo Fisher 16050–122 Sodium pyruvate Thermo Fisher 11360–039 D-Glucose solution 45% Sigma-Aldrich G8769 GlutaMAX Thermo Fisher 35050061 B27 Supplement Thermo Fisher 17504–044 Neurobasal Medium Thermo Fisher 21103–049 Penicillin-Streptomycin Thermo Fisher 15140–122 Lipofectamine 2000 Transfection Reagent Thermo Fisher 11668019 Matrigel Growth Factor Reduced Corning 354230 Essential 8 Medium Thermo Fisher A1517001 ReLeSR Stemcell Technologies 05872 Accutase Sigma-Aldrich A6964 ROCK Inhibitor Y-27632 Selleckchem S1049 Knockout Serum Replacement Thermo Fisher 10828010 DMEM/F-12, HEPES Thermo Fisher 11330032 N2 Supplement Thermo Fisher 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher 11140050 Doxycycline Sigma-Aldrich D9891 Poly-L-Ornithine Sigma-Aldrich P3655 BrainPhys Neuronal Medium Stemcell Technologies 05790 Lipofectamine STEM Transfection Reagent Thermo Fisher STEM00003 Laminin Corning 354232 BDNF PeproTech 450–02 NT-3 PeproTech 450–03 Microcystin-LR Sigma-Aldrich 475815 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher 78442 Pepstatin A Sigma-Aldrich P5318 E64d Sigma-Aldrich E8640 5-Fluoro-2′-deoxyuridine Sigma-Aldrich F0503 Uridine Sigma-Aldrich U3003 EveryBlot Blocking Buffer BioRad 12010020 Critical commercial assays BCA Protein Assay Kit Thermo Fisher 23225 ZymoPURE II Plasmid Maxiprep Kit ZymoResearch D4203 (Continued on next page) Cell Reports 45, 117364, June 23, 2026 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: cell lines Human: KOLF2.1J WT iPSCs B. Skarnes (Jackson Laboratories, Connecticut) RRID: CVCL_B5P3 Human: KOLF2.1J LRRK2-R1441H iPSCs B. Skarnes (Jackson Laboratories, Connecticut) N/A Human: KOLF2.1J PPM1H KO iPSCs Dou et al.13 RRID: CVCL_C7TY Experimental models: organisms/strains Mouse: LRRK2-G2019S knock-in Taconic 13940 Mouse: C57BL/6NTac WT Taconic B6 Mouse: PPM1H knock-out Taconic TF3142 Recombinant DNA Plasmid: CMV mScarlet-LC3B Modified from EGFP-LC3B (gift from T. Yoshimori, Osaka University, Japan) Addgene plasmid #200431 Plasmid: PGK mCherry-LC3B Modified from pLEX PGK mCherry-LC3B (gift from Michael Ward, NIH) N/A Plasmid: CMV SEP-LAMP1-RFP Gift from J. Bonifacino (NIH) Addgene plasmid #167970 Plasmid: CMV aSyn-EGFP VectorBuilder, same linker as described in56 VB230227-1242vtx Plasmid: PGK aSyn-EGFP VectorBuilder, same linker as described in56 VB251105-1468fsr Plasmid: PB-TO-hNGN2 Gift from iPSC Neurodegenerative Disease Initiative (iNDI) & Michael Ward Addgene plasmid #172115 Plasmid: piggyBacTM transposase vector Transposagen N/A Software and algorithms FIJI (Release 2.9.0) NIH, USA http://fiji.sc Prism 10 GraphPad https://www.graphpad.com/ scientific-software/prism/ RStudio: Integrated Development for R (2022.07.0) RStudio Team http://www.rstudio.com/ R package: nlme Pinheiro J, Bates D, R Core Team http://CRAN.R-project.org/package=nlme R package: lme4 Bates D, Mächler M, Bolker B, Walker S https://cran.r-project.org/web/ packages/lme4/index.html MATLAB R2022a MathWorks https://www.mathworks.com/ products/matlab.html KymoSuite (custom MATLAB script) Guedes-Dias et al.57 https://github.com/jnirschl/kinesin- 3_guedes-dias_2018/tree/master/kymoSuite, https://zenodo.org/record/2530934 VisiView Visitron https://www.visitron.de/products/ visiviewr-software.html ZEN blue Zeiss https://www.zeiss.com/microscopy/ en/products/software/zeiss-zen.html Image Studio LI-COR https://www.licor.com/bio/image-studio/ Adobe Illustrator 2023 Adobe https://www.adobe.com/ products/illustrator.html BioRender BioRender https://biorender.com/ Other 35 mm #1.5 glass bottom imaging dishes MatTek P35G-1.5-20-C 12 mm #1.5 glass coverslips R. Langenbrinck GmbH 01-0012/5 ProLong Gold Antifade Mountant Thermo Fisher P36930 16 Cell Reports 45, 117364, June 23, 2026
Bicinchoninic Acid Protein Assay:Article Title: Knockout of the LRRK2-counteracting RAB phosphatase PPM1H disrupts axonal autophagy and exacerbates alpha-synuclein aggregation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-RAB10 antibody, Mouse Monoclonal Nanotools 0680-100/Rab10-605B11; RRID: AB_2921226 Anti-RAB10 (phospho T73) antibody, Rabbit Monoclonal Abcam ab230261; RRID: AB_2811274 Anti-RAB12 antibody, Mouse Monoclonal Santa Cruz Biotechnology sc-515613; RRID: AB_3101762 Anti-RAB12 (phospho S106), Rabbit Monoclonal Abcam ab256487; RRID: AB_2884880 Anti-PPM1H antibody, Sheep Polyclonal MRC PPU reagents and services, University of Dundee, Scotland DA018, 3rd bleed; RRID: AB_2923281 Anti-LRRK2 antibody, Rabbit Monoclonal Abcam ab133474; RRID: AB_2713963 Anti-αSynuclein antibody, Rabbit Monoclonal Cell Signaling 4179; RRID: AB_1904156 Anti-Rabbit IgG-IRDye 800CW, Donkey Polyclonal Li-COR Biosciences 926-32213; RRID: AB_621848 Anti-Mouse IgG-IRDye 680RD, Donkey Polyclonal Li-COR Biosciences 926-68073; RRID: AB_10954442 Anti-Sheep Alexa Fluor 680, Donkey Polyclonal Thermo Fisher A21102; RRID: AB_10374469 Anti-αSynuclein (phospho S129) antibody, Rabbit Monoclonal Abcam ab51253; RRID: AB_869973 Anti-αSynuclein (phospho S129) antibody, Mouse Monoclonal BioLegend 825701; RRID: AB_2564891 Anti-LC3 antibody, Rabbit Polyclonal Abcam ab48394; RRID: AB_881433 Anti-GABARAP/L1/L2 antibody, Rabbit Monoclonal Abcam ab109364; RRID: AB_10861928 Anti-αSynuclein antibody, Mouse Monoclonal BD 610787; RRID: AB_398108 Anti-Synapsin1/2 antibody, Rabbit Polyclonal Synaptic Systems 106002; RRID: AB_887804 Anti-Bassoon antibody, Guinea Pig Monoclonal Synaptic Systems 141318; RRID: AB_2927388 Anti-Homer1 antibody, Rabbit Polyclonal Synaptic Systems 160003; RRID: AB_887730 Anti-MAP2 antibody, Mouse Monoclonal Millipore MAB3418; RRID: AB_94856 Anti-MAP2 antibody, Chicken Polyclonal Abcam ab5392; RRID: AB_2138153 Anti-Chicken Alexa Fluor 405, Goat Polyclonal Thermo Fisher A-48260; RRID: AB_2890271 Anti-Rabbit Alexa Fluor 488, Goat Polyclonal Thermo Fisher A-11034; RRID: AB_2576217 Anti-Mouse Alexa Fluor 488, Goat Polyclonal Thermo Fisher A-11001; RRID: AB_2534069 Anti-Mouse Alexa Fluor 594, Goat Polyclonal Thermo Fisher A-11005; RRID: AB_2534073 (Continued on next page) 14 Cell Reports 45, 117364, June 23, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Mouse Alexa Fluor 546, Goat Polyclonal Thermo Fisher A-11030; RRID: AB_2737024 Anti-Chicken Alexa Fluor 647, Goat Polyclonal Thermo Fisher A-21449; RRID: AB_2535866 Anti-Rabbit Alexa Fluor 647, Goat Polyclonal Thermo Fisher A-21245; RRID: AB_2535813 Chemicals, peptides, and recombinant proteins MLi-2 Tocris 5756 DMSO AppliChem A3672,0100 Poly-L-Lysine (mol wt 70,000–150,000) Sigma-Aldrich P1274 HBSS (10x) Thermo Fisher 14185–052 1M HEPES Thermo Fisher 15630–080 2.5% Trypsin Thermo Fisher 15090–046 Minimum essential medium (MEM) Thermo Fisher 11095–072 Horse serum (heat inactivated) Thermo Fisher 16050–122 Sodium pyruvate Thermo Fisher 11360–039 D-Glucose solution 45% Sigma-Aldrich G8769 GlutaMAX Thermo Fisher 35050061 B27 Supplement Thermo Fisher 17504–044 Neurobasal Medium Thermo Fisher 21103–049 Penicillin-Streptomycin Thermo Fisher 15140–122 Lipofectamine 2000 Transfection Reagent Thermo Fisher 11668019 Matrigel Growth Factor Reduced Corning 354230 Essential 8 Medium Thermo Fisher A1517001 ReLeSR Stemcell Technologies 05872 Accutase Sigma-Aldrich A6964 ROCK Inhibitor Y-27632 Selleckchem S1049 Knockout Serum Replacement Thermo Fisher 10828010 DMEM/F-12, HEPES Thermo Fisher 11330032 N2 Supplement Thermo Fisher 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher 11140050 Doxycycline Sigma-Aldrich D9891 Poly-L-Ornithine Sigma-Aldrich P3655 BrainPhys Neuronal Medium Stemcell Technologies 05790 Lipofectamine STEM Transfection Reagent Thermo Fisher STEM00003 Laminin Corning 354232 BDNF PeproTech 450–02 NT-3 PeproTech 450–03 Microcystin-LR Sigma-Aldrich 475815 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher 78442 Pepstatin A Sigma-Aldrich P5318 E64d Sigma-Aldrich E8640 5-Fluoro-2′-deoxyuridine Sigma-Aldrich F0503 Uridine Sigma-Aldrich U3003 EveryBlot Blocking Buffer BioRad 12010020 Critical commercial assays BCA Protein Assay Kit Thermo Fisher 23225 ZymoPURE II Plasmid Maxiprep Kit ZymoResearch D4203 (Continued on next page) Cell Reports 45, 117364, June 23, 2026 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: cell lines Human: KOLF2.1J WT iPSCs B. Skarnes (Jackson Laboratories, Connecticut) RRID: CVCL_B5P3 Human: KOLF2.1J LRRK2-R1441H iPSCs B. Skarnes (Jackson Laboratories, Connecticut) N/A Human: KOLF2.1J PPM1H KO iPSCs Dou et al.13 RRID: CVCL_C7TY Experimental models: organisms/strains Mouse: LRRK2-G2019S knock-in Taconic 13940 Mouse: C57BL/6NTac WT Taconic B6 Mouse: PPM1H knock-out Taconic TF3142 Recombinant DNA Plasmid: CMV mScarlet-LC3B Modified from EGFP-LC3B (gift from T. Yoshimori, Osaka University, Japan) Addgene plasmid #200431 Plasmid: PGK mCherry-LC3B Modified from pLEX PGK mCherry-LC3B (gift from Michael Ward, NIH) N/A Plasmid: CMV SEP-LAMP1-RFP Gift from J. Bonifacino (NIH) Addgene plasmid #167970 Plasmid: CMV aSyn-EGFP VectorBuilder, same linker as described in56 VB230227-1242vtx Plasmid: PGK aSyn-EGFP VectorBuilder, same linker as described in56 VB251105-1468fsr Plasmid: PB-TO-hNGN2 Gift from iPSC Neurodegenerative Disease Initiative (iNDI) & Michael Ward Addgene plasmid #172115 Plasmid: piggyBacTM transposase vector Transposagen N/A Software and algorithms FIJI (Release 2.9.0) NIH, USA http://fiji.sc Prism 10 GraphPad https://www.graphpad.com/ scientific-software/prism/ RStudio: Integrated Development for R (2022.07.0) RStudio Team http://www.rstudio.com/ R package: nlme Pinheiro J, Bates D, R Core Team http://CRAN.R-project.org/package=nlme R package: lme4 Bates D, Mächler M, Bolker B, Walker S https://cran.r-project.org/web/ packages/lme4/index.html MATLAB R2022a MathWorks https://www.mathworks.com/ products/matlab.html KymoSuite (custom MATLAB script) Guedes-Dias et al.57 https://github.com/jnirschl/kinesin- 3_guedes-dias_2018/tree/master/kymoSuite, https://zenodo.org/record/2530934 VisiView Visitron https://www.visitron.de/products/ visiviewr-software.html ZEN blue Zeiss https://www.zeiss.com/microscopy/ en/products/software/zeiss-zen.html Image Studio LI-COR https://www.licor.com/bio/image-studio/ Adobe Illustrator 2023 Adobe https://www.adobe.com/ products/illustrator.html BioRender BioRender https://biorender.com/ Other 35 mm #1.5 glass bottom imaging dishes MatTek P35G-1.5-20-C 12 mm #1.5 glass coverslips R. Langenbrinck GmbH 01-0012/5 ProLong Gold Antifade Mountant Thermo Fisher P36930 16 Cell Reports 45, 117364, June 23, 2026
Plasmid Preparation:Article Title: Knockout of the LRRK2-counteracting RAB phosphatase PPM1H disrupts axonal autophagy and exacerbates alpha-synuclein aggregation.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-RAB10 antibody, Mouse Monoclonal Nanotools 0680-100/Rab10-605B11; RRID: AB_2921226 Anti-RAB10 (phospho T73) antibody, Rabbit Monoclonal Abcam ab230261; RRID: AB_2811274 Anti-RAB12 antibody, Mouse Monoclonal Santa Cruz Biotechnology sc-515613; RRID: AB_3101762 Anti-RAB12 (phospho S106), Rabbit Monoclonal Abcam ab256487; RRID: AB_2884880 Anti-PPM1H antibody, Sheep Polyclonal MRC PPU reagents and services, University of Dundee, Scotland DA018, 3rd bleed; RRID: AB_2923281 Anti-LRRK2 antibody, Rabbit Monoclonal Abcam ab133474; RRID: AB_2713963 Anti-αSynuclein antibody, Rabbit Monoclonal Cell Signaling 4179; RRID: AB_1904156 Anti-Rabbit IgG-IRDye 800CW, Donkey Polyclonal Li-COR Biosciences 926-32213; RRID: AB_621848 Anti-Mouse IgG-IRDye 680RD, Donkey Polyclonal Li-COR Biosciences 926-68073; RRID: AB_10954442 Anti-Sheep Alexa Fluor 680, Donkey Polyclonal Thermo Fisher A21102; RRID: AB_10374469 Anti-αSynuclein (phospho S129) antibody, Rabbit Monoclonal Abcam ab51253; RRID: AB_869973 Anti-αSynuclein (phospho S129) antibody, Mouse Monoclonal BioLegend 825701; RRID: AB_2564891 Anti-LC3 antibody, Rabbit Polyclonal Abcam ab48394; RRID: AB_881433 Anti-GABARAP/L1/L2 antibody, Rabbit Monoclonal Abcam ab109364; RRID: AB_10861928 Anti-αSynuclein antibody, Mouse Monoclonal BD 610787; RRID: AB_398108 Anti-Synapsin1/2 antibody, Rabbit Polyclonal Synaptic Systems 106002; RRID: AB_887804 Anti-Bassoon antibody, Guinea Pig Monoclonal Synaptic Systems 141318; RRID: AB_2927388 Anti-Homer1 antibody, Rabbit Polyclonal Synaptic Systems 160003; RRID: AB_887730 Anti-MAP2 antibody, Mouse Monoclonal Millipore MAB3418; RRID: AB_94856 Anti-MAP2 antibody, Chicken Polyclonal Abcam ab5392; RRID: AB_2138153 Anti-Chicken Alexa Fluor 405, Goat Polyclonal Thermo Fisher A-48260; RRID: AB_2890271 Anti-Rabbit Alexa Fluor 488, Goat Polyclonal Thermo Fisher A-11034; RRID: AB_2576217 Anti-Mouse Alexa Fluor 488, Goat Polyclonal Thermo Fisher A-11001; RRID: AB_2534069 Anti-Mouse Alexa Fluor 594, Goat Polyclonal Thermo Fisher A-11005; RRID: AB_2534073 (Continued on next page) 14 Cell Reports 45, 117364, June 23, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Mouse Alexa Fluor 546, Goat Polyclonal Thermo Fisher A-11030; RRID: AB_2737024 Anti-Chicken Alexa Fluor 647, Goat Polyclonal Thermo Fisher A-21449; RRID: AB_2535866 Anti-Rabbit Alexa Fluor 647, Goat Polyclonal Thermo Fisher A-21245; RRID: AB_2535813 Chemicals, peptides, and recombinant proteins MLi-2 Tocris 5756 DMSO AppliChem A3672,0100 Poly-L-Lysine (mol wt 70,000–150,000) Sigma-Aldrich P1274 HBSS (10x) Thermo Fisher 14185–052 1M HEPES Thermo Fisher 15630–080 2.5% Trypsin Thermo Fisher 15090–046 Minimum essential medium (MEM) Thermo Fisher 11095–072 Horse serum (heat inactivated) Thermo Fisher 16050–122 Sodium pyruvate Thermo Fisher 11360–039 D-Glucose solution 45% Sigma-Aldrich G8769 GlutaMAX Thermo Fisher 35050061 B27 Supplement Thermo Fisher 17504–044 Neurobasal Medium Thermo Fisher 21103–049 Penicillin-Streptomycin Thermo Fisher 15140–122 Lipofectamine 2000 Transfection Reagent Thermo Fisher 11668019 Matrigel Growth Factor Reduced Corning 354230 Essential 8 Medium Thermo Fisher A1517001 ReLeSR Stemcell Technologies 05872 Accutase Sigma-Aldrich A6964 ROCK Inhibitor Y-27632 Selleckchem S1049 Knockout Serum Replacement Thermo Fisher 10828010 DMEM/F-12, HEPES Thermo Fisher 11330032 N2 Supplement Thermo Fisher 17502048 Non-essential Amino Acids (NEAA) Thermo Fisher 11140050 Doxycycline Sigma-Aldrich D9891 Poly-L-Ornithine Sigma-Aldrich P3655 BrainPhys Neuronal Medium Stemcell Technologies 05790 Lipofectamine STEM Transfection Reagent Thermo Fisher STEM00003 Laminin Corning 354232 BDNF PeproTech 450–02 NT-3 PeproTech 450–03 Microcystin-LR Sigma-Aldrich 475815 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher 78442 Pepstatin A Sigma-Aldrich P5318 E64d Sigma-Aldrich E8640 5-Fluoro-2′-deoxyuridine Sigma-Aldrich F0503 Uridine Sigma-Aldrich U3003 EveryBlot Blocking Buffer BioRad 12010020 Critical commercial assays BCA Protein Assay Kit Thermo Fisher 23225 ZymoPURE II Plasmid Maxiprep Kit ZymoResearch D4203 (Continued on next page) Cell Reports 45, 117364, June 23, 2026 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: cell lines Human: KOLF2.1J WT iPSCs B. Skarnes (Jackson Laboratories, Connecticut) RRID: CVCL_B5P3 Human: KOLF2.1J LRRK2-R1441H iPSCs B. Skarnes (Jackson Laboratories, Connecticut) N/A Human: KOLF2.1J PPM1H KO iPSCs Dou et al.13 RRID: CVCL_C7TY Experimental models: organisms/strains Mouse: LRRK2-G2019S knock-in Taconic 13940 Mouse: C57BL/6NTac WT Taconic B6 Mouse: PPM1H knock-out Taconic TF3142 Recombinant DNA Plasmid: CMV mScarlet-LC3B Modified from EGFP-LC3B (gift from T. Yoshimori, Osaka University, Japan) Addgene plasmid #200431 Plasmid: PGK mCherry-LC3B Modified from pLEX PGK mCherry-LC3B (gift from Michael Ward, NIH) N/A Plasmid: CMV SEP-LAMP1-RFP Gift from J. Bonifacino (NIH) Addgene plasmid #167970 Plasmid: CMV aSyn-EGFP VectorBuilder, same linker as described in56 VB230227-1242vtx Plasmid: PGK aSyn-EGFP VectorBuilder, same linker as described in56 VB251105-1468fsr Plasmid: PB-TO-hNGN2 Gift from iPSC Neurodegenerative Disease Initiative (iNDI) & Michael Ward Addgene plasmid #172115 Plasmid: piggyBacTM transposase vector Transposagen N/A Software and algorithms FIJI (Release 2.9.0) NIH, USA http://fiji.sc Prism 10 GraphPad https://www.graphpad.com/ scientific-software/prism/ RStudio: Integrated Development for R (2022.07.0) RStudio Team http://www.rstudio.com/ R package: nlme Pinheiro J, Bates D, R Core Team http://CRAN.R-project.org/package=nlme R package: lme4 Bates D, Mächler M, Bolker B, Walker S https://cran.r-project.org/web/ packages/lme4/index.html MATLAB R2022a MathWorks https://www.mathworks.com/ products/matlab.html KymoSuite (custom MATLAB script) Guedes-Dias et al.57 https://github.com/jnirschl/kinesin- 3_guedes-dias_2018/tree/master/kymoSuite, https://zenodo.org/record/2530934 VisiView Visitron https://www.visitron.de/products/ visiviewr-software.html ZEN blue Zeiss https://www.zeiss.com/microscopy/ en/products/software/zeiss-zen.html Image Studio LI-COR https://www.licor.com/bio/image-studio/ Adobe Illustrator 2023 Adobe https://www.adobe.com/ products/illustrator.html BioRender BioRender https://biorender.com/ Other 35 mm #1.5 glass bottom imaging dishes MatTek P35G-1.5-20-C 12 mm #1.5 glass coverslips R. Langenbrinck GmbH 01-0012/5 ProLong Gold Antifade Mountant Thermo Fisher P36930 16 Cell Reports 45, 117364, June 23, 2026
Flow Cytometry:Article Title: Multiplex genome editing eliminates lactate production without impacting growth rate in mammalian cells
Article Snippet: 0-F5 and Lama2 knockout CHO-S cells (which are not expected to have an altered metabolic phenotype) were thawed and maintained in CD CHO medium supplemented with 8 mM glutamine (Thermo-Fisher Scientific, Cat. # 25030024) and 1:500 PVA (Acros Organics, Cat. # 180300010) as an anti-clumping agent. .. After recovery, cells were counted using a Guava benchtop flow cytometry and stained using Guava ViaCount, (Luminex, Cat. # 4000–0040), centrifuged at 1000 × g for 5 minutes and resuspended in 2 mL of assay media (Seahorse XF base medium without phenol red (Agilent, Cat. # 103334–100), 1 mM pyruvate (Acros Organics, Cat. # 132151000), 2 mM glutamine, 10 mM glucose (Agilent, Cat. # 103577–100), 5 mM HEPES (Agilent, Cat. # 103337–100). .. Cells were plated in Seahorse 96 well plates (Agilent, Cat. # 103729–100) previously coated with Corning Cell Tak cell adhesive (Corning, Cat. # 10317081) following manufacturer’s instructions and analyzed using the Seahorse XF Glycolytic Rate Assay (Agilent, Cat. # 103344–100) following manufacturer’s instructions.
Article Title: Multiplex genome editing eliminates the Warburg Effect without impacting growth rate in mammalian cells
Article Snippet: 0-F5 and Lama2 knockout CHO-S cells (which are not expected to have an altered metabolic phenotype) were thawed and maintained in CD CHO medium supplemented with 8 mM glutamine (Thermo-Fisher Scientific, Cat. # 25030024) and 1:500 PVA (Acros Organics, Cat. # 180300010) as an anti-clumping agent. .. After recovery, cells were counted using a Guava benchtop flow cytometry and stained using Guava ViaCount, (Luminex, Cat. # 4000-0040), centrifuged at 1000 x g for 5 minutes and resuspended in 2 mL of assay media (Seahorse XF base medium without phenol red (Agilent, Cat. # 103334-100), 1 mM pyruvate (Acros Organics, Cat. # 132151000), 2 mM glutamine, 10 mM glucose (Agilent, Cat. # 103577-100), 5 mM HEPES (Agilent, Cat. # 103337-100 ). .. Cells were plated in Seahorse 96 well plates (Agilent, Cat. # 103729-100) previously coated with Corning Cell Tak cell adhesive (Corning, Cat. # 10317081) following manufacturer’s instructions and analyzed using the Seahorse XF Glycolytic Rate Assay (Agilent, Cat. # 103344-100) following manufacturer’s instructions.
Staining:Article Title: Multiplex genome editing eliminates lactate production without impacting growth rate in mammalian cells
Article Snippet: 0-F5 and Lama2 knockout CHO-S cells (which are not expected to have an altered metabolic phenotype) were thawed and maintained in CD CHO medium supplemented with 8 mM glutamine (Thermo-Fisher Scientific, Cat. # 25030024) and 1:500 PVA (Acros Organics, Cat. # 180300010) as an anti-clumping agent. .. After recovery, cells were counted using a Guava benchtop flow cytometry and stained using Guava ViaCount, (Luminex, Cat. # 4000–0040), centrifuged at 1000 × g for 5 minutes and resuspended in 2 mL of assay media (Seahorse XF base medium without phenol red (Agilent, Cat. # 103334–100), 1 mM pyruvate (Acros Organics, Cat. # 132151000), 2 mM glutamine, 10 mM glucose (Agilent, Cat. # 103577–100), 5 mM HEPES (Agilent, Cat. # 103337–100). .. Cells were plated in Seahorse 96 well plates (Agilent, Cat. # 103729–100) previously coated with Corning Cell Tak cell adhesive (Corning, Cat. # 10317081) following manufacturer’s instructions and analyzed using the Seahorse XF Glycolytic Rate Assay (Agilent, Cat. # 103344–100) following manufacturer’s instructions.
Article Title: Protocol for antibody-dependent cellular phagocytosis assay with controlled IgG concentrations in tested samples.
Article Snippet: .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Anti-human IgG Fab-specific, 1 mg/mL SouthernBiotech 2085-01 Biological samples Serum from vaccinated seropositive individuals FHCC IRB#10453 Serum from Seattle-area seroepidemiology study participants University of Washington NCT04338360 Pooled anti-SARS-CoV-2 serum University of Washington NCT04344977 Chemicals, peptides, and recombinant proteins RPMI 1640 Gibco 11875-093 Sodium pyruvate Gibco 11360-070 Sodium bicarbonate Gibco 25080-094 HEPES Gibco 15630-080 PenStrep Gibco 15070-063 Fetal bovine serum (FBS) HyClone SH30071.03 Phosphate-buffered solution (PBS) Gibco 14190-144 Tween-20 Sigma-Aldrich P7949-500ML Sodium Azide Millipore Sigma S8032 Paraformaldehyde Boster AR1068 Sulfo-NHS-LC-biotin Thermo Scientific A39257 Sulfo-NHS Thermo Scientific A39269 EDC Thermo Scientific 77149 Trypan Blue stain Invitrogen T10282 Experimental models: Cell lines THP-1 monocytes ATCC TIB-202 Software and algorithms GraphPad Prism GraphPad Software https://www.graphpad.com/how-to-buy/ FlowJo BD Biosciences https://www.flowjo.com/flowjo/download Bio-Plex Manager Bio-Rad https://www.bio-rad.com/en-us/product/ bio-plex-manager-software-standard- edition?ID=5846e84e-03a7-4599a8ae-7ba5dd2c7684 Other Zeba spin desalting column Thermo Scientific 89882 Bio-Plex ProTM Flat Bottom Plates Bio-Rad 171025001 Blotting-grade blocker Bio-Rad 1706404 Tissue Culture Plates, 96-well, U-bottom Genesee Scientific 25-221 NeutrAvidin-labeled microspheres Invitrogen F8776 Bovine serum albumin SAFC Biosciences B4287-100G Bio-Plex Pro Magnetic COOH beads Bio-Rad MC10027-01 Bio-Plex 200 System Bio-Rad N/A BCP Wash buffer Reagent Final concentration Amount Tween-20 (25%) 0.05% 0.4 mL NaN 3 (10%) 0.1% 2 mL Bovine serum albumin 10 mg/mL 2 g PBS N/A 195.6 mL Total N/A 200 mL [Store at room temperature, maximum storage time of 1 month or prepare fresh per experiment]. ..
Article Title: Multiplex genome editing eliminates the Warburg Effect without impacting growth rate in mammalian cells
Article Snippet: 0-F5 and Lama2 knockout CHO-S cells (which are not expected to have an altered metabolic phenotype) were thawed and maintained in CD CHO medium supplemented with 8 mM glutamine (Thermo-Fisher Scientific, Cat. # 25030024) and 1:500 PVA (Acros Organics, Cat. # 180300010) as an anti-clumping agent. .. After recovery, cells were counted using a Guava benchtop flow cytometry and stained using Guava ViaCount, (Luminex, Cat. # 4000-0040), centrifuged at 1000 x g for 5 minutes and resuspended in 2 mL of assay media (Seahorse XF base medium without phenol red (Agilent, Cat. # 103334-100), 1 mM pyruvate (Acros Organics, Cat. # 132151000), 2 mM glutamine, 10 mM glucose (Agilent, Cat. # 103577-100), 5 mM HEPES (Agilent, Cat. # 103337-100 ). .. Cells were plated in Seahorse 96 well plates (Agilent, Cat. # 103729-100) previously coated with Corning Cell Tak cell adhesive (Corning, Cat. # 10317081) following manufacturer’s instructions and analyzed using the Seahorse XF Glycolytic Rate Assay (Agilent, Cat. # 103344-100) following manufacturer’s instructions.
Data-independent acquisition:Article Title: Lactate determination with ferric ions in biological liquids is restricted to high concentrations or samples with controlled composition
Article Snippet: .. In this study we used ~90 % L‐lactic acid solution (Ap‐ pliChem, Germany), sodium D‐lactate ≥ 99 % (Sigma‐ Aldrich, USA); pyruvic acid sodium salt ≥ 99 % (Acros organics, USA); sodium chloride USP grade ≥ 99.5 % (Helicon, Russia), fermented peptone (DIA‐M, Rus‐ sia); yeast extract without salt, type D 95.2 % (DIA‐M, Russia); purum amino acids: threonine, valine, glu‐ tamic acid, leucine, isoleucine, alanine, methionine, glutamine, glycine, phenylalanine, arginine, lysine (“AO REACHIM”, Russia); iron(III) chloride hexahydrate pu‐ rified, and ddH2O. ..
Software:Article Title: Protocol for antibody-dependent cellular phagocytosis assay with controlled IgG concentrations in tested samples.
Article Snippet: .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Anti-human IgG Fab-specific, 1 mg/mL SouthernBiotech 2085-01 Biological samples Serum from vaccinated seropositive individuals FHCC IRB#10453 Serum from Seattle-area seroepidemiology study participants University of Washington NCT04338360 Pooled anti-SARS-CoV-2 serum University of Washington NCT04344977 Chemicals, peptides, and recombinant proteins RPMI 1640 Gibco 11875-093 Sodium pyruvate Gibco 11360-070 Sodium bicarbonate Gibco 25080-094 HEPES Gibco 15630-080 PenStrep Gibco 15070-063 Fetal bovine serum (FBS) HyClone SH30071.03 Phosphate-buffered solution (PBS) Gibco 14190-144 Tween-20 Sigma-Aldrich P7949-500ML Sodium Azide Millipore Sigma S8032 Paraformaldehyde Boster AR1068 Sulfo-NHS-LC-biotin Thermo Scientific A39257 Sulfo-NHS Thermo Scientific A39269 EDC Thermo Scientific 77149 Trypan Blue stain Invitrogen T10282 Experimental models: Cell lines THP-1 monocytes ATCC TIB-202 Software and algorithms GraphPad Prism GraphPad Software https://www.graphpad.com/how-to-buy/ FlowJo BD Biosciences https://www.flowjo.com/flowjo/download Bio-Plex Manager Bio-Rad https://www.bio-rad.com/en-us/product/ bio-plex-manager-software-standard- edition?ID=5846e84e-03a7-4599a8ae-7ba5dd2c7684 Other Zeba spin desalting column Thermo Scientific 89882 Bio-Plex ProTM Flat Bottom Plates Bio-Rad 171025001 Blotting-grade blocker Bio-Rad 1706404 Tissue Culture Plates, 96-well, U-bottom Genesee Scientific 25-221 NeutrAvidin-labeled microspheres Invitrogen F8776 Bovine serum albumin SAFC Biosciences B4287-100G Bio-Plex Pro Magnetic COOH beads Bio-Rad MC10027-01 Bio-Plex 200 System Bio-Rad N/A BCP Wash buffer Reagent Final concentration Amount Tween-20 (25%) 0.05% 0.4 mL NaN 3 (10%) 0.1% 2 mL Bovine serum albumin 10 mg/mL 2 g PBS N/A 195.6 mL Total N/A 200 mL [Store at room temperature, maximum storage time of 1 month or prepare fresh per experiment]. ..
Concentration Assay:Article Title: Protocol for antibody-dependent cellular phagocytosis assay with controlled IgG concentrations in tested samples.
Article Snippet: .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Anti-human IgG Fab-specific, 1 mg/mL SouthernBiotech 2085-01 Biological samples Serum from vaccinated seropositive individuals FHCC IRB#10453 Serum from Seattle-area seroepidemiology study participants University of Washington NCT04338360 Pooled anti-SARS-CoV-2 serum University of Washington NCT04344977 Chemicals, peptides, and recombinant proteins RPMI 1640 Gibco 11875-093 Sodium pyruvate Gibco 11360-070 Sodium bicarbonate Gibco 25080-094 HEPES Gibco 15630-080 PenStrep Gibco 15070-063 Fetal bovine serum (FBS) HyClone SH30071.03 Phosphate-buffered solution (PBS) Gibco 14190-144 Tween-20 Sigma-Aldrich P7949-500ML Sodium Azide Millipore Sigma S8032 Paraformaldehyde Boster AR1068 Sulfo-NHS-LC-biotin Thermo Scientific A39257 Sulfo-NHS Thermo Scientific A39269 EDC Thermo Scientific 77149 Trypan Blue stain Invitrogen T10282 Experimental models: Cell lines THP-1 monocytes ATCC TIB-202 Software and algorithms GraphPad Prism GraphPad Software https://www.graphpad.com/how-to-buy/ FlowJo BD Biosciences https://www.flowjo.com/flowjo/download Bio-Plex Manager Bio-Rad https://www.bio-rad.com/en-us/product/ bio-plex-manager-software-standard- edition?ID=5846e84e-03a7-4599a8ae-7ba5dd2c7684 Other Zeba spin desalting column Thermo Scientific 89882 Bio-Plex ProTM Flat Bottom Plates Bio-Rad 171025001 Blotting-grade blocker Bio-Rad 1706404 Tissue Culture Plates, 96-well, U-bottom Genesee Scientific 25-221 NeutrAvidin-labeled microspheres Invitrogen F8776 Bovine serum albumin SAFC Biosciences B4287-100G Bio-Plex Pro Magnetic COOH beads Bio-Rad MC10027-01 Bio-Plex 200 System Bio-Rad N/A BCP Wash buffer Reagent Final concentration Amount Tween-20 (25%) 0.05% 0.4 mL NaN 3 (10%) 0.1% 2 mL Bovine serum albumin 10 mg/mL 2 g PBS N/A 195.6 mL Total N/A 200 mL [Store at room temperature, maximum storage time of 1 month or prepare fresh per experiment]. ..
Activation Assay:
Cell Culture:
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