Journal: NPJ Systems Biology and Applications

Article Title: Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs

doi: 10.1038/s41540-024-00364-2

Figure Lengend Snippet: a UMAP of 25,775 cells colored by cell type. b Metacell distribution across cell type space for each time point. Metacells are red while single cells are grey. c Violin plot of the number of genes detected for SEACell-generated metacells (top) compared to all single cells (bottom). d Box plots showing metacell purity for each day. The lower and upper hinges of the boxplots represent the first and third quartiles, the center line is the median, and the whiskers extend no further than 1.5 * interquartile range.

Article Snippet: Fig. 3 Summary of sMetacell output. a UMAP of 25,775 cells colored by cell type. b Metacell distribution across cell type space for each time point.

Techniques: Generated

Journal: Acta Neuropathologica Communications

Article Title: Spatio-temporal dynamics of microglia phenotype in human and murine cSVD: impact of acute and chronic hypertensive states

doi: 10.1186/s40478-023-01672-0

Figure Lengend Snippet: Chronic hypertension results in microglia dynamical changes in the hippocampus of hypertensive rats. Overlay of Uniform manifold approximation and projection (UMAP) map displaying randomly sub-sampled microglia cells from normotensive and hypertensive hippocampus analyzed by flow cytometry in ( a ) early and ( e ) late hypertension. ( b , f ) UMAP plot with color-coded Phenograph-guided clustering with cell identities established based on the investigated surface markers. Representative UMAP plots from normotensive and hypertensive brains displaying microglia sub-clusters corresponding to each cohort. ( c , g ) Relative frequencies of microglial cells and their respective percentages per cluster in early and late chronic hypertension. ( d , h ) Heat map displaying normalized median expression values for each population present in each color-coded cluster exhibiting dynamic expression of diverse microglia activation markers (CD200R, CD45, CD86, CD163, MHCII, CD11b/c, P2Y12R, CX3CR1) upon early and late chronic hypertension compared to their respective age-matched normotensive control. Ctrl, Controls; HTN, Hypertension. p -values: ** for p ≤ 0.01; *** for p ≤ 0.001; **** for p ≤ 0.0001

Article Snippet: Flowjo UMAP and Phenograph plugins.

Techniques: Flow Cytometry, Expressing, Activation Assay

Journal: eBioMedicine

Article Title: Genomic profiling and associated B cell lineages delineate the efficacy of neoadjuvant anti-PD-1-based therapy in oesophageal squamous cell carcinoma

doi: 10.1016/j.ebiom.2024.104971

Figure Lengend Snippet: Immune infiltration heterogeneity of ESCC with distinct therapeutic responses. (a) UMAP plot showing clustering for immune cells from 10 patients with ESCC (left), expression of selected genes (middle) and distribution according to different therapeutic responses (right). (b) Dot plot showing the expression of PDCD1 and CD274 in immune cell clusters from responders and non-responders. (c) Lollipop chart showing difference of proportions of immune cell clusters in patients with different MMR status (left) and therapeutic responses (right) (scales of circles indicate the –log P value; Student's t test). (d) Expression heatmap of signature genes in distinct lymphocyte clusters. (e) UMAP plot showing the subclustering for CD4 + T cells from 10 patients with ESCC (left), expression of selected genes (middle) and distribution in different therapeutic responses (right). (f) Lollipop chart showing differences of proportions of CD4 + T cell subclusters from patients with different MMR status (left) and therapeutic responses (right) (scales of circles indicate the –log P value; Student's t test). (g) UMAP plot showing the subclustering for B cells from 10 patients with ESCC (left), expression of selected genes (middle) and distribution according to different therapeutic responses (right). (h) Lollipop and column chart showing difference of proportions of B cell subclusters from patients with different MMR status (scales of circles indicate the –log P value; Student's t test; left) and therapeutic responses (Chi-square test; right). P values are indicated in the figure.

Article Snippet: Immune infiltration heterogeneity of ESCC with distinct therapeutic responses. (a) UMAP plot showing clustering for immune cells from 10 patients with ESCC (left), expression of selected genes (middle) and distribution according to different therapeutic responses (right). (b) Dot plot showing the expression of PDCD1 and CD274 in immune cell clusters from responders and non-responders. (c) Lollipop chart showing difference of proportions of immune cell clusters in patients with different MMR status (left) and therapeutic responses (right) (scales of circles indicate the –log P value; Student's t test). (d) Expression heatmap of signature genes in distinct lymphocyte clusters. (e) UMAP plot showing the subclustering for CD4 + T cells from 10 patients with ESCC (left), expression of selected genes (middle) and distribution in different therapeutic responses (right). (f) Lollipop chart showing differences of proportions of CD4 + T cell subclusters from patients with different MMR status (left) and therapeutic responses (right) (scales of circles indicate the –log P value; Student's t test). (g) UMAP plot showing the subclustering for B cells from 10 patients with ESCC (left), expression of selected genes (middle) and distribution according to different therapeutic responses (right). (h) Lollipop and column chart showing difference of proportions of B cell subclusters from patients with different MMR status (scales of circles indicate the –log P value; Student's t test; left) and therapeutic responses (Chi-square test; right).

Techniques: Expressing