Blocking Assay:Article Title: Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
Article Snippet: .. Various Various Human TruStain FcX (Fc Receptor Blocking Solution) Biolegend Cat#422301 Chemicals, peptides, and recombinant proteins Collagenase IV Worthington Cat#LS004188 Deoxyribonuclease I Sigma-Aldrich Cat#DN25 cis-Diammineplatinum(II) dichloride (Cisplatin) Sigma-Aldrich Cat#P4394 Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15710 Zombie Aqua Fixable Viability Dye Thermo Fisher Cat#L34966 Candor PBS Antibody Stabilization solution Candor Bioscience Cat#13150 Maxpar 10X Barcode Perm Buffer Fluidigm Cat#201057 Cell-ID Intercalator-IR Fluidigm Cat201192A Maxpar Cell Acquisition Solution Fluidigm Cat#201240 Target Retrieval Solution Dako Agilent Cat#S1699 PBS IHC Wash Buffer + Tween 20 Cell Marque Cat#934B-06 EQ Four Element Calibration Beads Fluidigm Cat#201078 ACK Lysing Buffer Thermo Fisher Cat#A1049201 Cell Staining Buffer Biolegend Cat#420201 Normal Donkey Serum Sigma-Aldrich Cat#566460 Critical commercial assays Chromium Next GEM Single Cell 50 Library Kit 10X Genomics Cat#PN-1000265 Chromium Single Cell V(D)J Enrichment kit 10X Genomics Cat#PN-1000005 50 Feature Barcode Kit 10X Genomics Cat#PN-1000256 MaxPar X8 Antibody Labeling Kits Fluidigm Various Metal-Loaded MIBItags IonPath Various Avidin/Biotin Blocking System Biolegend Cat#927301 Deposited data Single-cell genomics data Generated by current investigators Deposited into GEO under accession number GSE212797 Mass cytometry and multiplexed ion beam imaging data Generated by current investigators Deposited into Mendeley Data under https://doi.org/10.17632/2zgppyr2rr.1 Software and algorithms R Core Team (v.4.0.5) The R Project for Statistical Computing https://www.r-project.org/ RStudio Posit https://posit.co/ Python (v.3.88) Python Software Foundation. .. Python Language Reference, version 3.8. http://www.python.org ParkerICI/Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa CellEngine CellCarta https://cellcarta.com/cellenginesoftware/ CytoNorm Van Gassen et al.65 https://github.com/saeyslab/CytoNorm Flowcore Ellis et al.66 https://bioconductor.org/packages/ release/bioc/html/flowCore.html (Continued on next page) e1 Cell 186, 1127–1143.e1–e7, March 16, 2023
Recombinant:Article Title: Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
Article Snippet: .. Various Various Human TruStain FcX (Fc Receptor Blocking Solution) Biolegend Cat#422301 Chemicals, peptides, and recombinant proteins Collagenase IV Worthington Cat#LS004188 Deoxyribonuclease I Sigma-Aldrich Cat#DN25 cis-Diammineplatinum(II) dichloride (Cisplatin) Sigma-Aldrich Cat#P4394 Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15710 Zombie Aqua Fixable Viability Dye Thermo Fisher Cat#L34966 Candor PBS Antibody Stabilization solution Candor Bioscience Cat#13150 Maxpar 10X Barcode Perm Buffer Fluidigm Cat#201057 Cell-ID Intercalator-IR Fluidigm Cat201192A Maxpar Cell Acquisition Solution Fluidigm Cat#201240 Target Retrieval Solution Dako Agilent Cat#S1699 PBS IHC Wash Buffer + Tween 20 Cell Marque Cat#934B-06 EQ Four Element Calibration Beads Fluidigm Cat#201078 ACK Lysing Buffer Thermo Fisher Cat#A1049201 Cell Staining Buffer Biolegend Cat#420201 Normal Donkey Serum Sigma-Aldrich Cat#566460 Critical commercial assays Chromium Next GEM Single Cell 50 Library Kit 10X Genomics Cat#PN-1000265 Chromium Single Cell V(D)J Enrichment kit 10X Genomics Cat#PN-1000005 50 Feature Barcode Kit 10X Genomics Cat#PN-1000256 MaxPar X8 Antibody Labeling Kits Fluidigm Various Metal-Loaded MIBItags IonPath Various Avidin/Biotin Blocking System Biolegend Cat#927301 Deposited data Single-cell genomics data Generated by current investigators Deposited into GEO under accession number GSE212797 Mass cytometry and multiplexed ion beam imaging data Generated by current investigators Deposited into Mendeley Data under https://doi.org/10.17632/2zgppyr2rr.1 Software and algorithms R Core Team (v.4.0.5) The R Project for Statistical Computing https://www.r-project.org/ RStudio Posit https://posit.co/ Python (v.3.88) Python Software Foundation. .. Python Language Reference, version 3.8. http://www.python.org ParkerICI/Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa CellEngine CellCarta https://cellcarta.com/cellenginesoftware/ CytoNorm Van Gassen et al.65 https://github.com/saeyslab/CytoNorm Flowcore Ellis et al.66 https://bioconductor.org/packages/ release/bioc/html/flowCore.html (Continued on next page) e1 Cell 186, 1127–1143.e1–e7, March 16, 2023
Electron Microscopy:Article Title: Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
Article Snippet: .. Various Various Human TruStain FcX (Fc Receptor Blocking Solution) Biolegend Cat#422301 Chemicals, peptides, and recombinant proteins Collagenase IV Worthington Cat#LS004188 Deoxyribonuclease I Sigma-Aldrich Cat#DN25 cis-Diammineplatinum(II) dichloride (Cisplatin) Sigma-Aldrich Cat#P4394 Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15710 Zombie Aqua Fixable Viability Dye Thermo Fisher Cat#L34966 Candor PBS Antibody Stabilization solution Candor Bioscience Cat#13150 Maxpar 10X Barcode Perm Buffer Fluidigm Cat#201057 Cell-ID Intercalator-IR Fluidigm Cat201192A Maxpar Cell Acquisition Solution Fluidigm Cat#201240 Target Retrieval Solution Dako Agilent Cat#S1699 PBS IHC Wash Buffer + Tween 20 Cell Marque Cat#934B-06 EQ Four Element Calibration Beads Fluidigm Cat#201078 ACK Lysing Buffer Thermo Fisher Cat#A1049201 Cell Staining Buffer Biolegend Cat#420201 Normal Donkey Serum Sigma-Aldrich Cat#566460 Critical commercial assays Chromium Next GEM Single Cell 50 Library Kit 10X Genomics Cat#PN-1000265 Chromium Single Cell V(D)J Enrichment kit 10X Genomics Cat#PN-1000005 50 Feature Barcode Kit 10X Genomics Cat#PN-1000256 MaxPar X8 Antibody Labeling Kits Fluidigm Various Metal-Loaded MIBItags IonPath Various Avidin/Biotin Blocking System Biolegend Cat#927301 Deposited data Single-cell genomics data Generated by current investigators Deposited into GEO under accession number GSE212797 Mass cytometry and multiplexed ion beam imaging data Generated by current investigators Deposited into Mendeley Data under https://doi.org/10.17632/2zgppyr2rr.1 Software and algorithms R Core Team (v.4.0.5) The R Project for Statistical Computing https://www.r-project.org/ RStudio Posit https://posit.co/ Python (v.3.88) Python Software Foundation. .. Python Language Reference, version 3.8. http://www.python.org ParkerICI/Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa CellEngine CellCarta https://cellcarta.com/cellenginesoftware/ CytoNorm Van Gassen et al.65 https://github.com/saeyslab/CytoNorm Flowcore Ellis et al.66 https://bioconductor.org/packages/ release/bioc/html/flowCore.html (Continued on next page) e1 Cell 186, 1127–1143.e1–e7, March 16, 2023
Immunohistochemistry:Article Title: Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
Article Snippet: .. Various Various Human TruStain FcX (Fc Receptor Blocking Solution) Biolegend Cat#422301 Chemicals, peptides, and recombinant proteins Collagenase IV Worthington Cat#LS004188 Deoxyribonuclease I Sigma-Aldrich Cat#DN25 cis-Diammineplatinum(II) dichloride (Cisplatin) Sigma-Aldrich Cat#P4394 Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15710 Zombie Aqua Fixable Viability Dye Thermo Fisher Cat#L34966 Candor PBS Antibody Stabilization solution Candor Bioscience Cat#13150 Maxpar 10X Barcode Perm Buffer Fluidigm Cat#201057 Cell-ID Intercalator-IR Fluidigm Cat201192A Maxpar Cell Acquisition Solution Fluidigm Cat#201240 Target Retrieval Solution Dako Agilent Cat#S1699 PBS IHC Wash Buffer + Tween 20 Cell Marque Cat#934B-06 EQ Four Element Calibration Beads Fluidigm Cat#201078 ACK Lysing Buffer Thermo Fisher Cat#A1049201 Cell Staining Buffer Biolegend Cat#420201 Normal Donkey Serum Sigma-Aldrich Cat#566460 Critical commercial assays Chromium Next GEM Single Cell 50 Library Kit 10X Genomics Cat#PN-1000265 Chromium Single Cell V(D)J Enrichment kit 10X Genomics Cat#PN-1000005 50 Feature Barcode Kit 10X Genomics Cat#PN-1000256 MaxPar X8 Antibody Labeling Kits Fluidigm Various Metal-Loaded MIBItags IonPath Various Avidin/Biotin Blocking System Biolegend Cat#927301 Deposited data Single-cell genomics data Generated by current investigators Deposited into GEO under accession number GSE212797 Mass cytometry and multiplexed ion beam imaging data Generated by current investigators Deposited into Mendeley Data under https://doi.org/10.17632/2zgppyr2rr.1 Software and algorithms R Core Team (v.4.0.5) The R Project for Statistical Computing https://www.r-project.org/ RStudio Posit https://posit.co/ Python (v.3.88) Python Software Foundation. .. Python Language Reference, version 3.8. http://www.python.org ParkerICI/Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa CellEngine CellCarta https://cellcarta.com/cellenginesoftware/ CytoNorm Van Gassen et al.65 https://github.com/saeyslab/CytoNorm Flowcore Ellis et al.66 https://bioconductor.org/packages/ release/bioc/html/flowCore.html (Continued on next page) e1 Cell 186, 1127–1143.e1–e7, March 16, 2023
Staining:Article Title: Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
Article Snippet: .. Various Various Human TruStain FcX (Fc Receptor Blocking Solution) Biolegend Cat#422301 Chemicals, peptides, and recombinant proteins Collagenase IV Worthington Cat#LS004188 Deoxyribonuclease I Sigma-Aldrich Cat#DN25 cis-Diammineplatinum(II) dichloride (Cisplatin) Sigma-Aldrich Cat#P4394 Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15710 Zombie Aqua Fixable Viability Dye Thermo Fisher Cat#L34966 Candor PBS Antibody Stabilization solution Candor Bioscience Cat#13150 Maxpar 10X Barcode Perm Buffer Fluidigm Cat#201057 Cell-ID Intercalator-IR Fluidigm Cat201192A Maxpar Cell Acquisition Solution Fluidigm Cat#201240 Target Retrieval Solution Dako Agilent Cat#S1699 PBS IHC Wash Buffer + Tween 20 Cell Marque Cat#934B-06 EQ Four Element Calibration Beads Fluidigm Cat#201078 ACK Lysing Buffer Thermo Fisher Cat#A1049201 Cell Staining Buffer Biolegend Cat#420201 Normal Donkey Serum Sigma-Aldrich Cat#566460 Critical commercial assays Chromium Next GEM Single Cell 50 Library Kit 10X Genomics Cat#PN-1000265 Chromium Single Cell V(D)J Enrichment kit 10X Genomics Cat#PN-1000005 50 Feature Barcode Kit 10X Genomics Cat#PN-1000256 MaxPar X8 Antibody Labeling Kits Fluidigm Various Metal-Loaded MIBItags IonPath Various Avidin/Biotin Blocking System Biolegend Cat#927301 Deposited data Single-cell genomics data Generated by current investigators Deposited into GEO under accession number GSE212797 Mass cytometry and multiplexed ion beam imaging data Generated by current investigators Deposited into Mendeley Data under https://doi.org/10.17632/2zgppyr2rr.1 Software and algorithms R Core Team (v.4.0.5) The R Project for Statistical Computing https://www.r-project.org/ RStudio Posit https://posit.co/ Python (v.3.88) Python Software Foundation. .. Python Language Reference, version 3.8. http://www.python.org ParkerICI/Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa CellEngine CellCarta https://cellcarta.com/cellenginesoftware/ CytoNorm Van Gassen et al.65 https://github.com/saeyslab/CytoNorm Flowcore Ellis et al.66 https://bioconductor.org/packages/ release/bioc/html/flowCore.html (Continued on next page) e1 Cell 186, 1127–1143.e1–e7, March 16, 2023
Single Cell:Article Title: Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
Article Snippet: .. Various Various Human TruStain FcX (Fc Receptor Blocking Solution) Biolegend Cat#422301 Chemicals, peptides, and recombinant proteins Collagenase IV Worthington Cat#LS004188 Deoxyribonuclease I Sigma-Aldrich Cat#DN25 cis-Diammineplatinum(II) dichloride (Cisplatin) Sigma-Aldrich Cat#P4394 Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15710 Zombie Aqua Fixable Viability Dye Thermo Fisher Cat#L34966 Candor PBS Antibody Stabilization solution Candor Bioscience Cat#13150 Maxpar 10X Barcode Perm Buffer Fluidigm Cat#201057 Cell-ID Intercalator-IR Fluidigm Cat201192A Maxpar Cell Acquisition Solution Fluidigm Cat#201240 Target Retrieval Solution Dako Agilent Cat#S1699 PBS IHC Wash Buffer + Tween 20 Cell Marque Cat#934B-06 EQ Four Element Calibration Beads Fluidigm Cat#201078 ACK Lysing Buffer Thermo Fisher Cat#A1049201 Cell Staining Buffer Biolegend Cat#420201 Normal Donkey Serum Sigma-Aldrich Cat#566460 Critical commercial assays Chromium Next GEM Single Cell 50 Library Kit 10X Genomics Cat#PN-1000265 Chromium Single Cell V(D)J Enrichment kit 10X Genomics Cat#PN-1000005 50 Feature Barcode Kit 10X Genomics Cat#PN-1000256 MaxPar X8 Antibody Labeling Kits Fluidigm Various Metal-Loaded MIBItags IonPath Various Avidin/Biotin Blocking System Biolegend Cat#927301 Deposited data Single-cell genomics data Generated by current investigators Deposited into GEO under accession number GSE212797 Mass cytometry and multiplexed ion beam imaging data Generated by current investigators Deposited into Mendeley Data under https://doi.org/10.17632/2zgppyr2rr.1 Software and algorithms R Core Team (v.4.0.5) The R Project for Statistical Computing https://www.r-project.org/ RStudio Posit https://posit.co/ Python (v.3.88) Python Software Foundation. .. Python Language Reference, version 3.8. http://www.python.org ParkerICI/Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa CellEngine CellCarta https://cellcarta.com/cellenginesoftware/ CytoNorm Van Gassen et al.65 https://github.com/saeyslab/CytoNorm Flowcore Ellis et al.66 https://bioconductor.org/packages/ release/bioc/html/flowCore.html (Continued on next page) e1 Cell 186, 1127–1143.e1–e7, March 16, 2023
Antibody Labeling:Article Title: Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
Article Snippet: .. Various Various Human TruStain FcX (Fc Receptor Blocking Solution) Biolegend Cat#422301 Chemicals, peptides, and recombinant proteins Collagenase IV Worthington Cat#LS004188 Deoxyribonuclease I Sigma-Aldrich Cat#DN25 cis-Diammineplatinum(II) dichloride (Cisplatin) Sigma-Aldrich Cat#P4394 Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15710 Zombie Aqua Fixable Viability Dye Thermo Fisher Cat#L34966 Candor PBS Antibody Stabilization solution Candor Bioscience Cat#13150 Maxpar 10X Barcode Perm Buffer Fluidigm Cat#201057 Cell-ID Intercalator-IR Fluidigm Cat201192A Maxpar Cell Acquisition Solution Fluidigm Cat#201240 Target Retrieval Solution Dako Agilent Cat#S1699 PBS IHC Wash Buffer + Tween 20 Cell Marque Cat#934B-06 EQ Four Element Calibration Beads Fluidigm Cat#201078 ACK Lysing Buffer Thermo Fisher Cat#A1049201 Cell Staining Buffer Biolegend Cat#420201 Normal Donkey Serum Sigma-Aldrich Cat#566460 Critical commercial assays Chromium Next GEM Single Cell 50 Library Kit 10X Genomics Cat#PN-1000265 Chromium Single Cell V(D)J Enrichment kit 10X Genomics Cat#PN-1000005 50 Feature Barcode Kit 10X Genomics Cat#PN-1000256 MaxPar X8 Antibody Labeling Kits Fluidigm Various Metal-Loaded MIBItags IonPath Various Avidin/Biotin Blocking System Biolegend Cat#927301 Deposited data Single-cell genomics data Generated by current investigators Deposited into GEO under accession number GSE212797 Mass cytometry and multiplexed ion beam imaging data Generated by current investigators Deposited into Mendeley Data under https://doi.org/10.17632/2zgppyr2rr.1 Software and algorithms R Core Team (v.4.0.5) The R Project for Statistical Computing https://www.r-project.org/ RStudio Posit https://posit.co/ Python (v.3.88) Python Software Foundation. .. Python Language Reference, version 3.8. http://www.python.org ParkerICI/Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa CellEngine CellCarta https://cellcarta.com/cellenginesoftware/ CytoNorm Van Gassen et al.65 https://github.com/saeyslab/CytoNorm Flowcore Ellis et al.66 https://bioconductor.org/packages/ release/bioc/html/flowCore.html (Continued on next page) e1 Cell 186, 1127–1143.e1–e7, March 16, 2023
Avidin-Biotin Assay:Article Title: Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
Article Snippet: .. Various Various Human TruStain FcX (Fc Receptor Blocking Solution) Biolegend Cat#422301 Chemicals, peptides, and recombinant proteins Collagenase IV Worthington Cat#LS004188 Deoxyribonuclease I Sigma-Aldrich Cat#DN25 cis-Diammineplatinum(II) dichloride (Cisplatin) Sigma-Aldrich Cat#P4394 Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15710 Zombie Aqua Fixable Viability Dye Thermo Fisher Cat#L34966 Candor PBS Antibody Stabilization solution Candor Bioscience Cat#13150 Maxpar 10X Barcode Perm Buffer Fluidigm Cat#201057 Cell-ID Intercalator-IR Fluidigm Cat201192A Maxpar Cell Acquisition Solution Fluidigm Cat#201240 Target Retrieval Solution Dako Agilent Cat#S1699 PBS IHC Wash Buffer + Tween 20 Cell Marque Cat#934B-06 EQ Four Element Calibration Beads Fluidigm Cat#201078 ACK Lysing Buffer Thermo Fisher Cat#A1049201 Cell Staining Buffer Biolegend Cat#420201 Normal Donkey Serum Sigma-Aldrich Cat#566460 Critical commercial assays Chromium Next GEM Single Cell 50 Library Kit 10X Genomics Cat#PN-1000265 Chromium Single Cell V(D)J Enrichment kit 10X Genomics Cat#PN-1000005 50 Feature Barcode Kit 10X Genomics Cat#PN-1000256 MaxPar X8 Antibody Labeling Kits Fluidigm Various Metal-Loaded MIBItags IonPath Various Avidin/Biotin Blocking System Biolegend Cat#927301 Deposited data Single-cell genomics data Generated by current investigators Deposited into GEO under accession number GSE212797 Mass cytometry and multiplexed ion beam imaging data Generated by current investigators Deposited into Mendeley Data under https://doi.org/10.17632/2zgppyr2rr.1 Software and algorithms R Core Team (v.4.0.5) The R Project for Statistical Computing https://www.r-project.org/ RStudio Posit https://posit.co/ Python (v.3.88) Python Software Foundation. .. Python Language Reference, version 3.8. http://www.python.org ParkerICI/Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa CellEngine CellCarta https://cellcarta.com/cellenginesoftware/ CytoNorm Van Gassen et al.65 https://github.com/saeyslab/CytoNorm Flowcore Ellis et al.66 https://bioconductor.org/packages/ release/bioc/html/flowCore.html (Continued on next page) e1 Cell 186, 1127–1143.e1–e7, March 16, 2023
Generated:Article Title: Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
Article Snippet: .. Various Various Human TruStain FcX (Fc Receptor Blocking Solution) Biolegend Cat#422301 Chemicals, peptides, and recombinant proteins Collagenase IV Worthington Cat#LS004188 Deoxyribonuclease I Sigma-Aldrich Cat#DN25 cis-Diammineplatinum(II) dichloride (Cisplatin) Sigma-Aldrich Cat#P4394 Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15710 Zombie Aqua Fixable Viability Dye Thermo Fisher Cat#L34966 Candor PBS Antibody Stabilization solution Candor Bioscience Cat#13150 Maxpar 10X Barcode Perm Buffer Fluidigm Cat#201057 Cell-ID Intercalator-IR Fluidigm Cat201192A Maxpar Cell Acquisition Solution Fluidigm Cat#201240 Target Retrieval Solution Dako Agilent Cat#S1699 PBS IHC Wash Buffer + Tween 20 Cell Marque Cat#934B-06 EQ Four Element Calibration Beads Fluidigm Cat#201078 ACK Lysing Buffer Thermo Fisher Cat#A1049201 Cell Staining Buffer Biolegend Cat#420201 Normal Donkey Serum Sigma-Aldrich Cat#566460 Critical commercial assays Chromium Next GEM Single Cell 50 Library Kit 10X Genomics Cat#PN-1000265 Chromium Single Cell V(D)J Enrichment kit 10X Genomics Cat#PN-1000005 50 Feature Barcode Kit 10X Genomics Cat#PN-1000256 MaxPar X8 Antibody Labeling Kits Fluidigm Various Metal-Loaded MIBItags IonPath Various Avidin/Biotin Blocking System Biolegend Cat#927301 Deposited data Single-cell genomics data Generated by current investigators Deposited into GEO under accession number GSE212797 Mass cytometry and multiplexed ion beam imaging data Generated by current investigators Deposited into Mendeley Data under https://doi.org/10.17632/2zgppyr2rr.1 Software and algorithms R Core Team (v.4.0.5) The R Project for Statistical Computing https://www.r-project.org/ RStudio Posit https://posit.co/ Python (v.3.88) Python Software Foundation. .. Python Language Reference, version 3.8. http://www.python.org ParkerICI/Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa CellEngine CellCarta https://cellcarta.com/cellenginesoftware/ CytoNorm Van Gassen et al.65 https://github.com/saeyslab/CytoNorm Flowcore Ellis et al.66 https://bioconductor.org/packages/ release/bioc/html/flowCore.html (Continued on next page) e1 Cell 186, 1127–1143.e1–e7, March 16, 2023
Mass Cytometry:Article Title: Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
Article Snippet: .. Various Various Human TruStain FcX (Fc Receptor Blocking Solution) Biolegend Cat#422301 Chemicals, peptides, and recombinant proteins Collagenase IV Worthington Cat#LS004188 Deoxyribonuclease I Sigma-Aldrich Cat#DN25 cis-Diammineplatinum(II) dichloride (Cisplatin) Sigma-Aldrich Cat#P4394 Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15710 Zombie Aqua Fixable Viability Dye Thermo Fisher Cat#L34966 Candor PBS Antibody Stabilization solution Candor Bioscience Cat#13150 Maxpar 10X Barcode Perm Buffer Fluidigm Cat#201057 Cell-ID Intercalator-IR Fluidigm Cat201192A Maxpar Cell Acquisition Solution Fluidigm Cat#201240 Target Retrieval Solution Dako Agilent Cat#S1699 PBS IHC Wash Buffer + Tween 20 Cell Marque Cat#934B-06 EQ Four Element Calibration Beads Fluidigm Cat#201078 ACK Lysing Buffer Thermo Fisher Cat#A1049201 Cell Staining Buffer Biolegend Cat#420201 Normal Donkey Serum Sigma-Aldrich Cat#566460 Critical commercial assays Chromium Next GEM Single Cell 50 Library Kit 10X Genomics Cat#PN-1000265 Chromium Single Cell V(D)J Enrichment kit 10X Genomics Cat#PN-1000005 50 Feature Barcode Kit 10X Genomics Cat#PN-1000256 MaxPar X8 Antibody Labeling Kits Fluidigm Various Metal-Loaded MIBItags IonPath Various Avidin/Biotin Blocking System Biolegend Cat#927301 Deposited data Single-cell genomics data Generated by current investigators Deposited into GEO under accession number GSE212797 Mass cytometry and multiplexed ion beam imaging data Generated by current investigators Deposited into Mendeley Data under https://doi.org/10.17632/2zgppyr2rr.1 Software and algorithms R Core Team (v.4.0.5) The R Project for Statistical Computing https://www.r-project.org/ RStudio Posit https://posit.co/ Python (v.3.88) Python Software Foundation. .. Python Language Reference, version 3.8. http://www.python.org ParkerICI/Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa CellEngine CellCarta https://cellcarta.com/cellenginesoftware/ CytoNorm Van Gassen et al.65 https://github.com/saeyslab/CytoNorm Flowcore Ellis et al.66 https://bioconductor.org/packages/ release/bioc/html/flowCore.html (Continued on next page) e1 Cell 186, 1127–1143.e1–e7, March 16, 2023
Imaging:Article Title: Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
Article Snippet: .. Various Various Human TruStain FcX (Fc Receptor Blocking Solution) Biolegend Cat#422301 Chemicals, peptides, and recombinant proteins Collagenase IV Worthington Cat#LS004188 Deoxyribonuclease I Sigma-Aldrich Cat#DN25 cis-Diammineplatinum(II) dichloride (Cisplatin) Sigma-Aldrich Cat#P4394 Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15710 Zombie Aqua Fixable Viability Dye Thermo Fisher Cat#L34966 Candor PBS Antibody Stabilization solution Candor Bioscience Cat#13150 Maxpar 10X Barcode Perm Buffer Fluidigm Cat#201057 Cell-ID Intercalator-IR Fluidigm Cat201192A Maxpar Cell Acquisition Solution Fluidigm Cat#201240 Target Retrieval Solution Dako Agilent Cat#S1699 PBS IHC Wash Buffer + Tween 20 Cell Marque Cat#934B-06 EQ Four Element Calibration Beads Fluidigm Cat#201078 ACK Lysing Buffer Thermo Fisher Cat#A1049201 Cell Staining Buffer Biolegend Cat#420201 Normal Donkey Serum Sigma-Aldrich Cat#566460 Critical commercial assays Chromium Next GEM Single Cell 50 Library Kit 10X Genomics Cat#PN-1000265 Chromium Single Cell V(D)J Enrichment kit 10X Genomics Cat#PN-1000005 50 Feature Barcode Kit 10X Genomics Cat#PN-1000256 MaxPar X8 Antibody Labeling Kits Fluidigm Various Metal-Loaded MIBItags IonPath Various Avidin/Biotin Blocking System Biolegend Cat#927301 Deposited data Single-cell genomics data Generated by current investigators Deposited into GEO under accession number GSE212797 Mass cytometry and multiplexed ion beam imaging data Generated by current investigators Deposited into Mendeley Data under https://doi.org/10.17632/2zgppyr2rr.1 Software and algorithms R Core Team (v.4.0.5) The R Project for Statistical Computing https://www.r-project.org/ RStudio Posit https://posit.co/ Python (v.3.88) Python Software Foundation. .. Python Language Reference, version 3.8. http://www.python.org ParkerICI/Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa CellEngine CellCarta https://cellcarta.com/cellenginesoftware/ CytoNorm Van Gassen et al.65 https://github.com/saeyslab/CytoNorm Flowcore Ellis et al.66 https://bioconductor.org/packages/ release/bioc/html/flowCore.html (Continued on next page) e1 Cell 186, 1127–1143.e1–e7, March 16, 2023
Software:Article Title: Dynamic CD8 + T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes.
Article Snippet: .. Various Various Human TruStain FcX (Fc Receptor Blocking Solution) Biolegend Cat#422301 Chemicals, peptides, and recombinant proteins Collagenase IV Worthington Cat#LS004188 Deoxyribonuclease I Sigma-Aldrich Cat#DN25 cis-Diammineplatinum(II) dichloride (Cisplatin) Sigma-Aldrich Cat#P4394 Paraformaldehyde aqueous solution Electron Microscopy Sciences Cat#15710 Zombie Aqua Fixable Viability Dye Thermo Fisher Cat#L34966 Candor PBS Antibody Stabilization solution Candor Bioscience Cat#13150 Maxpar 10X Barcode Perm Buffer Fluidigm Cat#201057 Cell-ID Intercalator-IR Fluidigm Cat201192A Maxpar Cell Acquisition Solution Fluidigm Cat#201240 Target Retrieval Solution Dako Agilent Cat#S1699 PBS IHC Wash Buffer + Tween 20 Cell Marque Cat#934B-06 EQ Four Element Calibration Beads Fluidigm Cat#201078 ACK Lysing Buffer Thermo Fisher Cat#A1049201 Cell Staining Buffer Biolegend Cat#420201 Normal Donkey Serum Sigma-Aldrich Cat#566460 Critical commercial assays Chromium Next GEM Single Cell 50 Library Kit 10X Genomics Cat#PN-1000265 Chromium Single Cell V(D)J Enrichment kit 10X Genomics Cat#PN-1000005 50 Feature Barcode Kit 10X Genomics Cat#PN-1000256 MaxPar X8 Antibody Labeling Kits Fluidigm Various Metal-Loaded MIBItags IonPath Various Avidin/Biotin Blocking System Biolegend Cat#927301 Deposited data Single-cell genomics data Generated by current investigators Deposited into GEO under accession number GSE212797 Mass cytometry and multiplexed ion beam imaging data Generated by current investigators Deposited into Mendeley Data under https://doi.org/10.17632/2zgppyr2rr.1 Software and algorithms R Core Team (v.4.0.5) The R Project for Statistical Computing https://www.r-project.org/ RStudio Posit https://posit.co/ Python (v.3.88) Python Software Foundation. .. Python Language Reference, version 3.8. http://www.python.org ParkerICI/Premessa Parker Institute for Cancer Immunotherapy https://github.com/ParkerICI/premessa CellEngine CellCarta https://cellcarta.com/cellenginesoftware/ CytoNorm Van Gassen et al.65 https://github.com/saeyslab/CytoNorm Flowcore Ellis et al.66 https://bioconductor.org/packages/ release/bioc/html/flowCore.html (Continued on next page) e1 Cell 186, 1127–1143.e1–e7, March 16, 2023
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