Journal: Scientific Reports

Article Title: Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos

doi: 10.1038/s41598-022-17127-w

Figure Lengend Snippet: The scRNA-seq analysis of etv2 ci32Gt ; UAS:GFP ; kdrl:mCherry embryos at the 24 hpf stage. ( A ) Schematics of the experimental design for scRNA-seq. ( B ) UMAP plot of 10,818 cells with 17 distinct clusters. Classifications were based on previously known marker genes which were significantly enriched in each cluster. RBC, red blood cells; VE, vascular endothelial; EPC, endothelial progenitor cells. ( C ) UMAP plot showing the distribution of GFP + mCherry + and GFP + mCherry- cells. ( D ) A heatmap showing expression of top marker genes in different clusters. Enlarged heatmap and gene list is shown in Fig. . ( E ) Fraction of GFP + mCherry + and GFP + mCherry- cells within each cluster. ( F ) A dot plot showing the expression of selected marker genes in different clusters.

Article Snippet: Finally, UMAP plots, violin plots, scatter plots, a dot plot, and a heatmap were obtained and exported from Partek.

Techniques: Marker, Expressing

Journal: Genome Biology

Article Title: Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis

doi: 10.1186/s13059-023-02908-x

Figure Lengend Snippet: Cell-type-specific regulatory networks and key regulators for root hair differentiation. a Mapping the information of chromatin openness revealed by snATAC-seq data into the cell clusters classified by snRNA-seq. b UMAP visualization of 10 cell clusters were annotated by both snRNA-seq and snATAC-seq for wheat root. Each dot represents a single cell. c High correlation between chromatin accessibility and expression of marker genes for each corresponding clusters. Left part is the open chromatin scores calculated based on snATAC-seq, Right part is the expression level calculated based on snRNA-seq. d Top5 representative TF regulons for each cluster identified by SCENIC4. The abbreviated names of TF regulons were followed with the chromosome name to indicate their location in subgenomes. e Root transections of taspl14 knock-out line and wild type. The protoxylem pores and companion cells were marked with yellow arrow and pink arrow head, respectively. Bar is 100 μm. f taspl14 knock-out line showed reduced companion cells and increased protoxylem. g BAM1 and LOB were downregulated in root of taspl14 knock-out lines. h The accessible chromatin regions (ACRs) of BAM1 homolog ( TraesCS4D02G235800 ). i Differentiated trajectories of root hair. Colors of dots are corresponding to cell clusters. Start indicates the initiation of the pseudo-time trajectory. Terminal indicates the end of the pseudo-time trajectory. j Trajectory network for root hair differentiation identified the key regulators for cell identity transition

Article Snippet: The 3D UMAP plot was visualized by R with Plotly package (v4.9.4.1).

Techniques: Expressing, Marker, Knock-Out

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