Journal: Cell

Article Title: A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

doi: 10.1016/j.cell.2018.08.039

Figure Lengend Snippet: Key resources table

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies A full list of antibodies is provided in Table S1 Biological Samples TNBC TMA was compiled by the Stanford Pathology Department Chemicals, Peptides, and Recombinant Proteins TBS IHC Wash Buffer with Tween 20 Cell Marque Cat#935B-09 PBS IHC Wash Buffer with Tween 20 Cell Marque Cat#934B-09 Target Retrieval Solution, pH 9, (3:1) Agilent (Dako) Cat#S2375 Avidin/Biotin Blocking Kit Biolegend Cat#927301 Gelatin (cold water fish skin) Sigma-Aldrich Cat#G7765–250 Xylene Histological grade Sigma-Aldrich Cat#534056–500 Glutaraldehyde 8% Aqueous Solution EM Grade EMS Cat#16020 Normal Donkey serum Sigma-Aldrich Cat#D9663–10ML Bovine Albumin (BSA) Fisher Cat#BP1600–100 Centrifugal filters (0.1 μm) Millipore Cat#UFC30VV00 Critical Commercial Assays Maxpar X8 Antibody labeling kit Fluidigm Cat2011XXX MIBItag Conjugation Kit IONpath Cat#600XXX ImmPRESS UNIVERSAL (Anti-Mouse/Anti-Rabbit) IgG KIT (HRP) Vector Laboratories Cat#MP-7500–15 ImmPACT DAB (For HRP Substrate) Vector Laboratories Cat#SK-4105 Deposited Data https://mibi-share.ionpath.com All the data of the study Software and Algorithms Data analysis was done using Matlab 2016 Mathworks https://github.com/lkeren/MIBIAnalysis Analysis code https://hub.docker.com/r/vanvalen/deepcell-mibi Segmentation code Open in a separate window Key resources table Multiplexed Imaging of subcellular expression of 36 proteins in 41 TNBC patients Enriched co-occurrence of immune populations define a structured immune environment Mixing of tumor and immune cells varies from Compartmentalized to Mixed patients Expression of PD-1 and PD-L1 by distinct cells relate to tumor histology and survival

Techniques: Recombinant, Avidin-Biotin Assay, Blocking Assay, Antibody Labeling, Conjugation Assay, Plasmid Preparation, Software

Journal: Cell

Article Title: A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

doi: 10.1016/j.cell.2018.08.039

Figure Lengend Snippet: Key resources table

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies A full list of antibodies is provided in Table S1 Biological Samples TNBC TMA was compiled by the Stanford Pathology Department Chemicals, Peptides, and Recombinant Proteins TBS IHC Wash Buffer with Tween 20 Cell Marque Cat#935B-09 PBS IHC Wash Buffer with Tween 20 Cell Marque Cat#934B-09 Target Retrieval Solution, pH 9, (3:1) Agilent (Dako) Cat#S2375 Avidin/Biotin Blocking Kit Biolegend Cat#927301 Gelatin (cold water fish skin) Sigma-Aldrich Cat#G7765–250 Xylene Histological grade Sigma-Aldrich Cat#534056–500 Glutaraldehyde 8% Aqueous Solution EM Grade EMS Cat#16020 Normal Donkey serum Sigma-Aldrich Cat#D9663–10ML Bovine Albumin (BSA) Fisher Cat#BP1600–100 Centrifugal filters (0.1 μm) Millipore Cat#UFC30VV00 Critical Commercial Assays Maxpar X8 Antibody labeling kit Fluidigm Cat#2011XXX MIBItag Conjugation Kit IONpath Cat#600XXX ImmPRESS UNIVERSAL (Anti-Mouse/Anti-Rabbit) IgG KIT (HRP) Vector Laboratories Cat#MP-7500–15 ImmPACT DAB (For HRP Substrate) Vector Laboratories Cat#SK-4105 Deposited Data https://mibi-share.ionpath.com All the data of the study Software and Algorithms Data analysis was done using Matlab 2016 Mathworks https://github.com/lkeren/MIBIAnalysis Analysis code https://hub.docker.com/r/vanvalen/deepcell-mibi Segmentation code Open in a separate window Key resources table Multiplexed Imaging of subcellular expression of 36 proteins in 41 TNBC patients Enriched co-occurrence of immune populations define a structured immune environment Mixing of tumor and immune cells varies from Compartmentalized to Mixed patients Expression of PD-1 and PD-L1 by distinct cells relate to tumor histology and survival

Techniques: Recombinant, Avidin-Biotin Assay, Blocking Assay, Antibody Labeling, Conjugation Assay, Plasmid Preparation, Software