flowsom plugin  (Tree Star Inc)

Journal: bioRxiv

Article Title: Transient inhibition of type I interferon enhances CD8 + T cell stemness and vaccine protection

doi: 10.1101/2024.06.26.600763

Figure Lengend Snippet: Analysis of P14 cells d8 or d14 of acute LCMV Armstrong, with or without IFNAR blocking at d0-1, or chronic LCMV Docile infection. Data representative of 3 independent experiments with 4 mice per group in each experiment. Each dot in (A, B, C, E) represent a single mouse. Data are mean ± S.E.M. Analyzed using one-way ANOVA tests. (A) Graphs summarizing the plaque forming units (PFU) from viable virus in spleens of mice in each infection condition. LOD dashed line indicates viral plaque limit of detection. (B) Graphs summarizing average frequencies of TIM-3 expression on P14 cells in each indicated group. (C) Graphs summarizing frequencies of stem-like (KLRG1 - SLAMF6 + ) T cell populations within P14 cells in each group. (D, E) FlowSOM dimensionality reduction analysis P14 cells generated in each infection condition. (D) FlowSOM dimensionality reduction analysis. tSNE plot displaying 5 FlowSOM defined cell populations and denoted identities generated from differential surface antigen expression. (E) Frequency of each FlowSOM population within d8 SLAMF6 + P14 cells for each infection condition, and corresponding representative overlay of SLAMF6 + P14 cells displayed in tSNE plots. **p<0.01, ***p<0.001, ****p<0.0001 Supplementary Figure 2 shows additional supporting data.

Article Snippet: All flow cytometry analysis was performed on a BD LSRFortessa X-20 and BD FACSymphony A3 Cell Analyzers (BD Biosciences) data was analyzed using FlowJo v10 (FlowJo LLC) and the FlowSOM plugin.

Techniques: Blocking Assay, Infection, Virus, Expressing, Generated

Journal: bioRxiv

Article Title: Transient inhibition of type I interferon enhances CD8 + T cell stemness and vaccine protection

doi: 10.1101/2024.06.26.600763

Figure Lengend Snippet: Related to . Analysis of P14 cells from peripheral lymph nodes of mice at d8 or d14 of acute LCMV Armstrong with or without IFNAR block at d0-1, or chronic LCMV Docile infection. Data representative of 3 independent experiments with 4 mice per group in each experiment. Each dot in (E) represent a single mouse. Data are mean ± S.E.M. Analyzed using one-way ANOVA tests. (A) Representative plots of TIM-3 expression on P14 cells within each infection condition. (B) Representative flow cytometry plots of T EFF (KLRG1 + SLAMF6 - ) and stem-like (KLRG1 - SLAMF6 + ) T cell populations within P14 cells from each group. (C) Overlay of marker expression heat maps on tSNE plot generated by FlowSOM. (D) FlowSOM heat map determining distinction of discreet populations. (E) Frequency of each FlowSOM population within d14 SLAMF6 + P14 cells for each infection condition, and corresponding representative overlay of SLAMF6 + P14 cells displayed in tSNE plots. *p<0.05, **p<0.01, ****p<0.0001

Article Snippet: All flow cytometry analysis was performed on a BD LSRFortessa X-20 and BD FACSymphony A3 Cell Analyzers (BD Biosciences) data was analyzed using FlowJo v10 (FlowJo LLC) and the FlowSOM plugin.

Techniques: Blocking Assay, Infection, Expressing, Flow Cytometry, Marker, Generated

Journal: Cell Reports Medicine

Article Title: Neoantigen-targeted dendritic cell vaccination in lung cancer patients induces long-lived T cells exhibiting the full differentiation spectrum

doi: 10.1016/j.xcrm.2024.101516

Figure Lengend Snippet:

Article Snippet: FlowSom plugin Flowjo (version 4.0.0) , FlowJo Software (for Windows) Version 10. Becton, Dickinson and Company; 2019. , https://www.flowjo.com/exchange/.

Techniques: Derivative Assay, Recombinant, Protease Inhibitor, Cell Isolation, Multiplexing, Sample Prep, Amplification, RNA Sequencing Assay, Software, Variant Assay, Sequencing, Chromatography, Transferring