Staining:Article Title: Pathological Angiogenesis Precedes the Onset of Aortic Dissection
Article Snippet: .. In brief, sections were deparaffinized and stained with anti-CD163-147Sm (#3147021D, Standard BioTools, South San Francisco, CA, USA), anti-collagen type I-169Tm (#3169023D, Standard BioTools), anti-Fibronectin-174Yb (#91H034174, Standard BioTools), anti-Alpha-Smooth Muscle Actin-209Bi (#3209017D, Standard BioTools), anti-CD206 (#87887SF, Cell Signaling Technology, Danvers, MA, USA) labeled with 141Pr (#201141A, Standard BioTools), anti-CD31 (#AF3628, R&D Systems) labeled with151Eu (#201151A, Standard BioTools), anti-ERG (ab214796, abcam) labeled with 153Eu (#201153A, Standard BioTools), anti-CD86 (#76755SF, Cell Signaling Technology) labeled with 158Gd (#201158A, Standard BioTools), anti-CD68 (#26042SF, Cell Signaling Technology) labeled with 159Tb (#201159A, Standard BioTools), anti-Ki67 (#87887SF, Cell Signaling Technology) labeled with 165Ho (#201165A, Standard BioTools), anti-CD14 (#43878SF, Cell Signaling Technology) labeled with 168Er (#201168A, Standard BioTools) and anti-Myeloperoxidase (#88757, Cell Signaling Technology) labeled with 175Lu (#201175A, Standard BioTools), following the manufacturer’s protocol. .. The tissue slide was ablated using a Hyperion Imaging System (Standard BioTools).
Labeling:Article Title: Pathological Angiogenesis Precedes the Onset of Aortic Dissection
Article Snippet: .. In brief, sections were deparaffinized and stained with anti-CD163-147Sm (#3147021D, Standard BioTools, South San Francisco, CA, USA), anti-collagen type I-169Tm (#3169023D, Standard BioTools), anti-Fibronectin-174Yb (#91H034174, Standard BioTools), anti-Alpha-Smooth Muscle Actin-209Bi (#3209017D, Standard BioTools), anti-CD206 (#87887SF, Cell Signaling Technology, Danvers, MA, USA) labeled with 141Pr (#201141A, Standard BioTools), anti-CD31 (#AF3628, R&D Systems) labeled with151Eu (#201151A, Standard BioTools), anti-ERG (ab214796, abcam) labeled with 153Eu (#201153A, Standard BioTools), anti-CD86 (#76755SF, Cell Signaling Technology) labeled with 158Gd (#201158A, Standard BioTools), anti-CD68 (#26042SF, Cell Signaling Technology) labeled with 159Tb (#201159A, Standard BioTools), anti-Ki67 (#87887SF, Cell Signaling Technology) labeled with 165Ho (#201165A, Standard BioTools), anti-CD14 (#43878SF, Cell Signaling Technology) labeled with 168Er (#201168A, Standard BioTools) and anti-Myeloperoxidase (#88757, Cell Signaling Technology) labeled with 175Lu (#201175A, Standard BioTools), following the manufacturer’s protocol. .. The tissue slide was ablated using a Hyperion Imaging System (Standard BioTools).
Antibody Labeling:
Article Title: Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline.
Article Snippet: .. 500 mL Thermo Fisher Scientific Cat#61870-010 eBioscience Protein Transport Inhibitor Cocktail (5003) Thermo Fisher Scientific Cat#00-4980-93 Proteomic Stabilizer PROT1 Smart Tube Inc. Cat#PROT1-1L Antibody Stabilizer PBS CANDOR Bioscience Cat#131 125 Sodium azide, ReagentPlus , R99.5% Sigma-Aldrich Cat#S2002-5G Bond-Breaker TCEP Solution, Neutral pH Thermo Fisher Scientific Cat#77720 Pierce 16% Formaldehyde (w/v), Methanol-free Thermo Scientific Cat#28908 Thaw-Lyse buffer Smart Tube Inc. Cat#PROT1-1L Heparin Sigma-Aldrich Cat#H3393-10KU Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat# D8418-100ml Dulbecco0s Phosphate Buffered Saline (DPBS) Fisher Scientific S.L Cat#14190-094 Critical commercial assays Maxpar X8 Antibody Labeling Kit, 154Sm—4 Rxn Standard BioTools Cat#201154A Maxpar X8 Antibody Labeling Kit, 160Gd—4 Rxn Standard BioTools Cat#201160A Maxpar X8 Antibody Labeling Kit, 170Er—4 Rxn Standard BioTools Cat#201170A Maxpar X8 Antibody Labeling Kit, 175Lu—4 Rxn Standard BioTools Cat201175A Deposited data FlowRepository: FR-FCM-Z3YR (Rybakowska et al., 2021a, 2021b) www.flowrepository.org (Continued on next page) ll OPEN ACCESS 14 STAR Protocols 3, 101697, December 16, 2022 Protocol Continued REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms CyTOF Software Version 6.7.1014 Standard BioTools https://www.fluidigm.com/software R software (R Core Team, 2013) http://www.R-project.org/ RStudio RStudio Team https://rstudio.com/ CytoQP This paper, https://doi.org/ 10.5281/zenodo.6947414 https://github.com/prybakowska/ CytoQP BiocParallel (Morgan et al., 2022b) https://bioconductor.org/packages/ release/bioc/html/BiocParallel.html WinRAR N/A https://www.win-rar.com/start.html?&L=12 Other Amicon Ultra-0.5 Centrifugal Filter Unit, 3 kDa Millipore Cat#UFC500396 Amicon Ultra-0.5 Centrifugal Filter Unit, 50 kDa Millipore Cat#UFC505096 MACS SmartStrainers (100 mm) Miltenyi Biotec Cat#130-110-917 TC20 Automated Cell Counter Bio-Rad Cat#1450102 Cell Counting Slides for TC10 /TC20 Cell Counter, Dual-Chamber, 30 slides, 60 counts Bio-Rad Cat#1450011 TC20 Data Analyzer Software Bio-Rad Cat#SOFT-TC20-Data-Analyzer Blood Collection tube, BD Vacutainer K2EDTA 10mL BD Cat# BDAM367525 Axygen 1.7 mL MaxyClear Snaplock Microcentrifuge Tube, Clear, Nonsterile, 500 Tubes/Pack, 10 Packs/Case Axygen Cat# MCT-175-C Eppendorf Safe-Lock Tubes, 0,5 mL, Eppendorf Quality , incoloro, 500 tubos. .. Eppendorf Cat#525-0129 Eppendorf Protein LoBind Tube, 1.5 mL Eppendorf Cat# 0224311081 5 mL polystyrene Round-bottom Tube (FACS tube) Fisher Scientific Cat#352054 HulaMixer Sample Mixer Thermo Fisher Scientific Cat#15920D Cytof2 upgraded to HELIOS Fluidigm N/A NB injector Fluidigm Cat#107018 HIMAC CT15RE tabletop centrifuges, HITACHI, Rotor T 15A61-1912 Himac centrifuges N/A VWR Digital microcentrifuges VWR2416 digital microcentrifuge, with 24 place rotor VWR Cat#521-2839 Centrifuge Mini Spin Eppendorf, fixed –angle rotor F45-12-11 Eppendorf Cat#521-0012 Multi-Purpose High Speed Centrifuges GYROZEN with Swing-Out Rotor GRS-G-r250-4 Gyrozen Cat# GZ-1248R Eppendorf Centrifuge 5702R Eppendorf Cat#EP022628012 Thermo Scientific Forma 900 Series 86 C Upright Ultra-Low Temperature Freezers Thermo Scientific Model# 9470E-907 Liebherr NoFrost Comfort Freezer Fisher Scientific Cat#15160333 Water-Jacketed, IR Autoflow Automatic CO2 Incubator, UN-4750E NuAire N/A Laminar Air Flow: Telstar bio II A Telstar N/A BradyR LABEXPERT printer Brady N/A Brady Polyester LABXPERT and IDXPERT Labels Brady Brand: Brady 806807 Fisherbrand S-Series Heated Ultrasonic Cleaning Bath (FB15046.)
Saline:Article Title: Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline.
Article Snippet: .. 500 mL Thermo Fisher Scientific Cat#61870-010 eBioscience Protein Transport Inhibitor Cocktail (5003) Thermo Fisher Scientific Cat#00-4980-93 Proteomic Stabilizer PROT1 Smart Tube Inc. Cat#PROT1-1L Antibody Stabilizer PBS CANDOR Bioscience Cat#131 125 Sodium azide, ReagentPlus , R99.5% Sigma-Aldrich Cat#S2002-5G Bond-Breaker TCEP Solution, Neutral pH Thermo Fisher Scientific Cat#77720 Pierce 16% Formaldehyde (w/v), Methanol-free Thermo Scientific Cat#28908 Thaw-Lyse buffer Smart Tube Inc. Cat#PROT1-1L Heparin Sigma-Aldrich Cat#H3393-10KU Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat# D8418-100ml Dulbecco0s Phosphate Buffered Saline (DPBS) Fisher Scientific S.L Cat#14190-094 Critical commercial assays Maxpar X8 Antibody Labeling Kit, 154Sm—4 Rxn Standard BioTools Cat#201154A Maxpar X8 Antibody Labeling Kit, 160Gd—4 Rxn Standard BioTools Cat#201160A Maxpar X8 Antibody Labeling Kit, 170Er—4 Rxn Standard BioTools Cat#201170A Maxpar X8 Antibody Labeling Kit, 175Lu—4 Rxn Standard BioTools Cat201175A Deposited data FlowRepository: FR-FCM-Z3YR (Rybakowska et al., 2021a, 2021b) www.flowrepository.org (Continued on next page) ll OPEN ACCESS 14 STAR Protocols 3, 101697, December 16, 2022 Protocol Continued REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms CyTOF Software Version 6.7.1014 Standard BioTools https://www.fluidigm.com/software R software (R Core Team, 2013) http://www.R-project.org/ RStudio RStudio Team https://rstudio.com/ CytoQP This paper, https://doi.org/ 10.5281/zenodo.6947414 https://github.com/prybakowska/ CytoQP BiocParallel (Morgan et al., 2022b) https://bioconductor.org/packages/ release/bioc/html/BiocParallel.html WinRAR N/A https://www.win-rar.com/start.html?&L=12 Other Amicon Ultra-0.5 Centrifugal Filter Unit, 3 kDa Millipore Cat#UFC500396 Amicon Ultra-0.5 Centrifugal Filter Unit, 50 kDa Millipore Cat#UFC505096 MACS SmartStrainers (100 mm) Miltenyi Biotec Cat#130-110-917 TC20 Automated Cell Counter Bio-Rad Cat#1450102 Cell Counting Slides for TC10 /TC20 Cell Counter, Dual-Chamber, 30 slides, 60 counts Bio-Rad Cat#1450011 TC20 Data Analyzer Software Bio-Rad Cat#SOFT-TC20-Data-Analyzer Blood Collection tube, BD Vacutainer K2EDTA 10mL BD Cat# BDAM367525 Axygen 1.7 mL MaxyClear Snaplock Microcentrifuge Tube, Clear, Nonsterile, 500 Tubes/Pack, 10 Packs/Case Axygen Cat# MCT-175-C Eppendorf Safe-Lock Tubes, 0,5 mL, Eppendorf Quality , incoloro, 500 tubos. .. Eppendorf Cat#525-0129 Eppendorf Protein LoBind Tube, 1.5 mL Eppendorf Cat# 0224311081 5 mL polystyrene Round-bottom Tube (FACS tube) Fisher Scientific Cat#352054 HulaMixer Sample Mixer Thermo Fisher Scientific Cat#15920D Cytof2 upgraded to HELIOS Fluidigm N/A NB injector Fluidigm Cat#107018 HIMAC CT15RE tabletop centrifuges, HITACHI, Rotor T 15A61-1912 Himac centrifuges N/A VWR Digital microcentrifuges VWR2416 digital microcentrifuge, with 24 place rotor VWR Cat#521-2839 Centrifuge Mini Spin Eppendorf, fixed –angle rotor F45-12-11 Eppendorf Cat#521-0012 Multi-Purpose High Speed Centrifuges GYROZEN with Swing-Out Rotor GRS-G-r250-4 Gyrozen Cat# GZ-1248R Eppendorf Centrifuge 5702R Eppendorf Cat#EP022628012 Thermo Scientific Forma 900 Series 86 C Upright Ultra-Low Temperature Freezers Thermo Scientific Model# 9470E-907 Liebherr NoFrost Comfort Freezer Fisher Scientific Cat#15160333 Water-Jacketed, IR Autoflow Automatic CO2 Incubator, UN-4750E NuAire N/A Laminar Air Flow: Telstar bio II A Telstar N/A BradyR LABEXPERT printer Brady N/A Brady Polyester LABXPERT and IDXPERT Labels Brady Brand: Brady 806807 Fisherbrand S-Series Heated Ultrasonic Cleaning Bath (FB15046.)
Software:Article Title: Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline.
Article Snippet: .. 500 mL Thermo Fisher Scientific Cat#61870-010 eBioscience Protein Transport Inhibitor Cocktail (5003) Thermo Fisher Scientific Cat#00-4980-93 Proteomic Stabilizer PROT1 Smart Tube Inc. Cat#PROT1-1L Antibody Stabilizer PBS CANDOR Bioscience Cat#131 125 Sodium azide, ReagentPlus , R99.5% Sigma-Aldrich Cat#S2002-5G Bond-Breaker TCEP Solution, Neutral pH Thermo Fisher Scientific Cat#77720 Pierce 16% Formaldehyde (w/v), Methanol-free Thermo Scientific Cat#28908 Thaw-Lyse buffer Smart Tube Inc. Cat#PROT1-1L Heparin Sigma-Aldrich Cat#H3393-10KU Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat# D8418-100ml Dulbecco0s Phosphate Buffered Saline (DPBS) Fisher Scientific S.L Cat#14190-094 Critical commercial assays Maxpar X8 Antibody Labeling Kit, 154Sm—4 Rxn Standard BioTools Cat#201154A Maxpar X8 Antibody Labeling Kit, 160Gd—4 Rxn Standard BioTools Cat#201160A Maxpar X8 Antibody Labeling Kit, 170Er—4 Rxn Standard BioTools Cat#201170A Maxpar X8 Antibody Labeling Kit, 175Lu—4 Rxn Standard BioTools Cat201175A Deposited data FlowRepository: FR-FCM-Z3YR (Rybakowska et al., 2021a, 2021b) www.flowrepository.org (Continued on next page) ll OPEN ACCESS 14 STAR Protocols 3, 101697, December 16, 2022 Protocol Continued REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms CyTOF Software Version 6.7.1014 Standard BioTools https://www.fluidigm.com/software R software (R Core Team, 2013) http://www.R-project.org/ RStudio RStudio Team https://rstudio.com/ CytoQP This paper, https://doi.org/ 10.5281/zenodo.6947414 https://github.com/prybakowska/ CytoQP BiocParallel (Morgan et al., 2022b) https://bioconductor.org/packages/ release/bioc/html/BiocParallel.html WinRAR N/A https://www.win-rar.com/start.html?&L=12 Other Amicon Ultra-0.5 Centrifugal Filter Unit, 3 kDa Millipore Cat#UFC500396 Amicon Ultra-0.5 Centrifugal Filter Unit, 50 kDa Millipore Cat#UFC505096 MACS SmartStrainers (100 mm) Miltenyi Biotec Cat#130-110-917 TC20 Automated Cell Counter Bio-Rad Cat#1450102 Cell Counting Slides for TC10 /TC20 Cell Counter, Dual-Chamber, 30 slides, 60 counts Bio-Rad Cat#1450011 TC20 Data Analyzer Software Bio-Rad Cat#SOFT-TC20-Data-Analyzer Blood Collection tube, BD Vacutainer K2EDTA 10mL BD Cat# BDAM367525 Axygen 1.7 mL MaxyClear Snaplock Microcentrifuge Tube, Clear, Nonsterile, 500 Tubes/Pack, 10 Packs/Case Axygen Cat# MCT-175-C Eppendorf Safe-Lock Tubes, 0,5 mL, Eppendorf Quality , incoloro, 500 tubos. .. Eppendorf Cat#525-0129 Eppendorf Protein LoBind Tube, 1.5 mL Eppendorf Cat# 0224311081 5 mL polystyrene Round-bottom Tube (FACS tube) Fisher Scientific Cat#352054 HulaMixer Sample Mixer Thermo Fisher Scientific Cat#15920D Cytof2 upgraded to HELIOS Fluidigm N/A NB injector Fluidigm Cat#107018 HIMAC CT15RE tabletop centrifuges, HITACHI, Rotor T 15A61-1912 Himac centrifuges N/A VWR Digital microcentrifuges VWR2416 digital microcentrifuge, with 24 place rotor VWR Cat#521-2839 Centrifuge Mini Spin Eppendorf, fixed –angle rotor F45-12-11 Eppendorf Cat#521-0012 Multi-Purpose High Speed Centrifuges GYROZEN with Swing-Out Rotor GRS-G-r250-4 Gyrozen Cat# GZ-1248R Eppendorf Centrifuge 5702R Eppendorf Cat#EP022628012 Thermo Scientific Forma 900 Series 86 C Upright Ultra-Low Temperature Freezers Thermo Scientific Model# 9470E-907 Liebherr NoFrost Comfort Freezer Fisher Scientific Cat#15160333 Water-Jacketed, IR Autoflow Automatic CO2 Incubator, UN-4750E NuAire N/A Laminar Air Flow: Telstar bio II A Telstar N/A BradyR LABEXPERT printer Brady N/A Brady Polyester LABXPERT and IDXPERT Labels Brady Brand: Brady 806807 Fisherbrand S-Series Heated Ultrasonic Cleaning Bath (FB15046.)
Magnetic Cell Separation:Article Title: Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline.
Article Snippet: .. 500 mL Thermo Fisher Scientific Cat#61870-010 eBioscience Protein Transport Inhibitor Cocktail (5003) Thermo Fisher Scientific Cat#00-4980-93 Proteomic Stabilizer PROT1 Smart Tube Inc. Cat#PROT1-1L Antibody Stabilizer PBS CANDOR Bioscience Cat#131 125 Sodium azide, ReagentPlus , R99.5% Sigma-Aldrich Cat#S2002-5G Bond-Breaker TCEP Solution, Neutral pH Thermo Fisher Scientific Cat#77720 Pierce 16% Formaldehyde (w/v), Methanol-free Thermo Scientific Cat#28908 Thaw-Lyse buffer Smart Tube Inc. Cat#PROT1-1L Heparin Sigma-Aldrich Cat#H3393-10KU Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat# D8418-100ml Dulbecco0s Phosphate Buffered Saline (DPBS) Fisher Scientific S.L Cat#14190-094 Critical commercial assays Maxpar X8 Antibody Labeling Kit, 154Sm—4 Rxn Standard BioTools Cat#201154A Maxpar X8 Antibody Labeling Kit, 160Gd—4 Rxn Standard BioTools Cat#201160A Maxpar X8 Antibody Labeling Kit, 170Er—4 Rxn Standard BioTools Cat#201170A Maxpar X8 Antibody Labeling Kit, 175Lu—4 Rxn Standard BioTools Cat201175A Deposited data FlowRepository: FR-FCM-Z3YR (Rybakowska et al., 2021a, 2021b) www.flowrepository.org (Continued on next page) ll OPEN ACCESS 14 STAR Protocols 3, 101697, December 16, 2022 Protocol Continued REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms CyTOF Software Version 6.7.1014 Standard BioTools https://www.fluidigm.com/software R software (R Core Team, 2013) http://www.R-project.org/ RStudio RStudio Team https://rstudio.com/ CytoQP This paper, https://doi.org/ 10.5281/zenodo.6947414 https://github.com/prybakowska/ CytoQP BiocParallel (Morgan et al., 2022b) https://bioconductor.org/packages/ release/bioc/html/BiocParallel.html WinRAR N/A https://www.win-rar.com/start.html?&L=12 Other Amicon Ultra-0.5 Centrifugal Filter Unit, 3 kDa Millipore Cat#UFC500396 Amicon Ultra-0.5 Centrifugal Filter Unit, 50 kDa Millipore Cat#UFC505096 MACS SmartStrainers (100 mm) Miltenyi Biotec Cat#130-110-917 TC20 Automated Cell Counter Bio-Rad Cat#1450102 Cell Counting Slides for TC10 /TC20 Cell Counter, Dual-Chamber, 30 slides, 60 counts Bio-Rad Cat#1450011 TC20 Data Analyzer Software Bio-Rad Cat#SOFT-TC20-Data-Analyzer Blood Collection tube, BD Vacutainer K2EDTA 10mL BD Cat# BDAM367525 Axygen 1.7 mL MaxyClear Snaplock Microcentrifuge Tube, Clear, Nonsterile, 500 Tubes/Pack, 10 Packs/Case Axygen Cat# MCT-175-C Eppendorf Safe-Lock Tubes, 0,5 mL, Eppendorf Quality , incoloro, 500 tubos. .. Eppendorf Cat#525-0129 Eppendorf Protein LoBind Tube, 1.5 mL Eppendorf Cat# 0224311081 5 mL polystyrene Round-bottom Tube (FACS tube) Fisher Scientific Cat#352054 HulaMixer Sample Mixer Thermo Fisher Scientific Cat#15920D Cytof2 upgraded to HELIOS Fluidigm N/A NB injector Fluidigm Cat#107018 HIMAC CT15RE tabletop centrifuges, HITACHI, Rotor T 15A61-1912 Himac centrifuges N/A VWR Digital microcentrifuges VWR2416 digital microcentrifuge, with 24 place rotor VWR Cat#521-2839 Centrifuge Mini Spin Eppendorf, fixed –angle rotor F45-12-11 Eppendorf Cat#521-0012 Multi-Purpose High Speed Centrifuges GYROZEN with Swing-Out Rotor GRS-G-r250-4 Gyrozen Cat# GZ-1248R Eppendorf Centrifuge 5702R Eppendorf Cat#EP022628012 Thermo Scientific Forma 900 Series 86 C Upright Ultra-Low Temperature Freezers Thermo Scientific Model# 9470E-907 Liebherr NoFrost Comfort Freezer Fisher Scientific Cat#15160333 Water-Jacketed, IR Autoflow Automatic CO2 Incubator, UN-4750E NuAire N/A Laminar Air Flow: Telstar bio II A Telstar N/A BradyR LABEXPERT printer Brady N/A Brady Polyester LABXPERT and IDXPERT Labels Brady Brand: Brady 806807 Fisherbrand S-Series Heated Ultrasonic Cleaning Bath (FB15046.)
Cell Counting:Article Title: Protocol for large scale whole blood immune monitoring by mass cytometry and Cyto Quality Pipeline.
Article Snippet: .. 500 mL Thermo Fisher Scientific Cat#61870-010 eBioscience Protein Transport Inhibitor Cocktail (5003) Thermo Fisher Scientific Cat#00-4980-93 Proteomic Stabilizer PROT1 Smart Tube Inc. Cat#PROT1-1L Antibody Stabilizer PBS CANDOR Bioscience Cat#131 125 Sodium azide, ReagentPlus , R99.5% Sigma-Aldrich Cat#S2002-5G Bond-Breaker TCEP Solution, Neutral pH Thermo Fisher Scientific Cat#77720 Pierce 16% Formaldehyde (w/v), Methanol-free Thermo Scientific Cat#28908 Thaw-Lyse buffer Smart Tube Inc. Cat#PROT1-1L Heparin Sigma-Aldrich Cat#H3393-10KU Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat# D8418-100ml Dulbecco0s Phosphate Buffered Saline (DPBS) Fisher Scientific S.L Cat#14190-094 Critical commercial assays Maxpar X8 Antibody Labeling Kit, 154Sm—4 Rxn Standard BioTools Cat#201154A Maxpar X8 Antibody Labeling Kit, 160Gd—4 Rxn Standard BioTools Cat#201160A Maxpar X8 Antibody Labeling Kit, 170Er—4 Rxn Standard BioTools Cat#201170A Maxpar X8 Antibody Labeling Kit, 175Lu—4 Rxn Standard BioTools Cat201175A Deposited data FlowRepository: FR-FCM-Z3YR (Rybakowska et al., 2021a, 2021b) www.flowrepository.org (Continued on next page) ll OPEN ACCESS 14 STAR Protocols 3, 101697, December 16, 2022 Protocol Continued REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms CyTOF Software Version 6.7.1014 Standard BioTools https://www.fluidigm.com/software R software (R Core Team, 2013) http://www.R-project.org/ RStudio RStudio Team https://rstudio.com/ CytoQP This paper, https://doi.org/ 10.5281/zenodo.6947414 https://github.com/prybakowska/ CytoQP BiocParallel (Morgan et al., 2022b) https://bioconductor.org/packages/ release/bioc/html/BiocParallel.html WinRAR N/A https://www.win-rar.com/start.html?&L=12 Other Amicon Ultra-0.5 Centrifugal Filter Unit, 3 kDa Millipore Cat#UFC500396 Amicon Ultra-0.5 Centrifugal Filter Unit, 50 kDa Millipore Cat#UFC505096 MACS SmartStrainers (100 mm) Miltenyi Biotec Cat#130-110-917 TC20 Automated Cell Counter Bio-Rad Cat#1450102 Cell Counting Slides for TC10 /TC20 Cell Counter, Dual-Chamber, 30 slides, 60 counts Bio-Rad Cat#1450011 TC20 Data Analyzer Software Bio-Rad Cat#SOFT-TC20-Data-Analyzer Blood Collection tube, BD Vacutainer K2EDTA 10mL BD Cat# BDAM367525 Axygen 1.7 mL MaxyClear Snaplock Microcentrifuge Tube, Clear, Nonsterile, 500 Tubes/Pack, 10 Packs/Case Axygen Cat# MCT-175-C Eppendorf Safe-Lock Tubes, 0,5 mL, Eppendorf Quality , incoloro, 500 tubos. .. Eppendorf Cat#525-0129 Eppendorf Protein LoBind Tube, 1.5 mL Eppendorf Cat# 0224311081 5 mL polystyrene Round-bottom Tube (FACS tube) Fisher Scientific Cat#352054 HulaMixer Sample Mixer Thermo Fisher Scientific Cat#15920D Cytof2 upgraded to HELIOS Fluidigm N/A NB injector Fluidigm Cat#107018 HIMAC CT15RE tabletop centrifuges, HITACHI, Rotor T 15A61-1912 Himac centrifuges N/A VWR Digital microcentrifuges VWR2416 digital microcentrifuge, with 24 place rotor VWR Cat#521-2839 Centrifuge Mini Spin Eppendorf, fixed –angle rotor F45-12-11 Eppendorf Cat#521-0012 Multi-Purpose High Speed Centrifuges GYROZEN with Swing-Out Rotor GRS-G-r250-4 Gyrozen Cat# GZ-1248R Eppendorf Centrifuge 5702R Eppendorf Cat#EP022628012 Thermo Scientific Forma 900 Series 86 C Upright Ultra-Low Temperature Freezers Thermo Scientific Model# 9470E-907 Liebherr NoFrost Comfort Freezer Fisher Scientific Cat#15160333 Water-Jacketed, IR Autoflow Automatic CO2 Incubator, UN-4750E NuAire N/A Laminar Air Flow: Telstar bio II A Telstar N/A BradyR LABEXPERT printer Brady N/A Brady Polyester LABXPERT and IDXPERT Labels Brady Brand: Brady 806807 Fisherbrand S-Series Heated Ultrasonic Cleaning Bath (FB15046.)
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