seurat tsne plots  (Partek)

Journal: Gastroenterology

Article Title: Combination of PD1 Inhibitor and OX40 Agonist Induces Tumor Rejection and Immune Memory in Mouse Models of Pancreatic Cancer

doi: 10.1053/j.gastro.2020.03.018

Figure Lengend Snippet: (A-E) tSNE plots of all T cells (A) with expression levels of CD4 (B), CD8 (C), NK1.1 (D), and PD-L1 (E) from all samples with number- and color-coded clusters.

Article Snippet: MATLAB for t-distributed stochastic neighbor embedding (tSNE) plot, heat map, and plot cluster tSNE.

Techniques: Expressing

Journal: Nature Communications

Article Title: TIM4 expression by dendritic cells mediates uptake of tumor-associated antigens and anti-tumor responses

doi: 10.1038/s41467-021-22535-z

Figure Lengend Snippet: a cDC1 were isolated from nLung or late KP tumors to analyze transcriptional profiles. The graph shows expression of cDC1 and cDC2 lineage specific genes in nLung-sorted and tumor-sorted cDC1. Data are expressed as mean ± SD with nLung n = 4, KP(l) n = 3. b Volcano plot showing the fold change of genes encoding scavenger receptors (significantly modulated genes are depicted in red and blue, using a q -value < 5%, a false discovery rate (FDR) ≤ 5% and a fold change ≥2 or ≤2), using the Significance Analysis of Microarray (SAM) algorithm. c The dot-plot shows the relative abundance of genes in b using a color and size scale of linear expression values. d T-distributed stochastic neighbor embedding (tSNE) plots of single cells expression profiles in mouse lungs (Tabula Muris). Colors represent clusters of different subsets based on global similarity of gene expression. The cluster corresponding to DC-macrophages was further analyzed to assess co-expression of cDC1 markers and Timd4 transcripts, as depicted in the boxes. e scRNA seq of naive and KP lung tumors from were analyzed to visualize Timd4 -expressing cells in three subpopulation of lung DCs. Violin plots show expression of Timd4 in cDC1, cDC2, and mregDCs. Statistical analysis was performed using Seurat R package, taking in consideration both number of expressing cells and levels of expression. f Representative histograms and quantification of the percentage of cells expressing TIM4 in nLung, early and late lung tumors (the gate for identification of positive and negative cells is depicted in the histogram). Data are from nLung n = 3, KP(e) n = 6, KP(l) n = 9 mice. Significance was determined by one-way ANOVA followed by Tukey’s post-test; data are expressed as mean ± SEM. g Representative histograms of TIM4 expression on total CD45 − and CD45 + cells and all lung phagocytic subsets in nLung and late KP lungs. Alveolar macrophages (AM), interstitial macrophages (IM), tumor associated macrophages (TAM), monocytes (Mono). Each peak is overlaid on the corresponding FMO controls (black line). Source data are provided as a Source Data file.

Article Snippet: Data are expressed as mean ± SD with nLung n = 4, KP(l) n = 3. b Volcano plot showing the fold change of genes encoding scavenger receptors (significantly modulated genes are depicted in red and blue, using a q -value < 5%, a false discovery rate (FDR) ≤ 5% and a fold change ≥2 or ≤2), using the Significance Analysis of Microarray (SAM) algorithm. c The dot-plot shows the relative abundance of genes in b using a color and size scale of linear expression values. d T-distributed stochastic neighbor embedding (tSNE) plots of single cells expression profiles in mouse lungs (Tabula Muris).

Techniques: Isolation, Expressing, Microarray, Gene Expression