umap plots  (MathWorks Inc)

Journal: iScience

Article Title: Imaging flow cytometry reveals divergent mitochondrial phenotypes in mitochondrial disease patients

doi: 10.1016/j.isci.2024.111496

Figure Lengend Snippet: Correlation of IFC features with phenotypic features (A) Correlation plot showing the correlation between IFC features and clinical phenotypes. All clinical features were converted to binary parameters (Yes = Present, No=Not present) and correlation was calculated using Spearman’s correlation. The color coding and dot size correlate with Spearman’s rho coefficient. (B) All significant correlations have been plotted as a boxplot. For the boxplots, the values of each of the five features ( Table 1 ) were normalized against the mean of the healthy control taken along within the same experiment and converted to percentages. Statistics were calculated using Welsch’s t test. The black line indicates the median value, the lower and upper hinges correspond to the 25th and 75th percentiles. The upper and lower whisker extend to 1.5∗IQR. (C) Showing the UMAP plots from Figures 2 C and A. The nodes are colored according to the presence of neuropathy (Yes, No, NA). NA means that the specific feature was not assessed in patients. Statistical significance between the two clusters was calculated using Fisher’s exact test. Neuropathy was the only clinical feature that had a significant association with one of the clusters.

Article Snippet: All graphs and UMAP plots were created using R-studio, except for the line chart of A, which was created with GraphPad Prism version 6 for Windows.

Techniques: Control, Whisker Assay

Journal: Scientific Reports

Article Title: Derivation of human primary prostate epithelial cell lines by differentially targeting the CDKN2A locus along with expression of hTERT

doi: 10.1038/s41598-024-71306-5

Figure Lengend Snippet: RNA-Seq Analysis showing gene expression and clustering of the immortalized cell lines and PrECs. ( a ) Principal Component Analysis (PCA) of the RNA-Seq data for all the clones and PrEC. ( b ) Prostate tissue UMAP plots obtained using scRNA-Seq by the Human Protein Atlas (with superimposed expression of Actin (ACTG1)) identify all distinct populations in the primary human prostate . ( c ) Gene expression heat map of predicted correlation scores (Preds) of each clone and hPrECs to the cell populations identified in the human prostate using scRNA-Seq. Prediction scores range from 0.0 to 1.0 (blue to dark red scale on the left). The distinct cell populations identified by the Human Atlas using single cell-RNA-Seq are labeled by color and a number (top of the heatmap and legend on the right). Clones and PrEC RNA-Seq samples were analyzed in triplicate. The prediction score in B indicate that the clones are most closely related to the basal prostatic population designated c2 (labeled red/orange in the first column of the heat map).

Article Snippet: Also, to establish what distinct cell populations were present in the parental PrECs, we used tools from the Human Protein Atlas database that utilizes UMAP plots obtained from prostate tissue single-cell RNA-Seq (scRNA-Seq) data to distinguish cell populations and expression patterns in prostate tissue cores .

Techniques: RNA Sequencing, Gene Expression, Clone Assay, Expressing, Labeling

Journal: Scientific Reports

Article Title: Derivation of human primary prostate epithelial cell lines by differentially targeting the CDKN2A locus along with expression of hTERT

doi: 10.1038/s41598-024-71306-5

Figure Lengend Snippet: RNA-Seq Analysis showing gene expression and clustering of the immortalized cell lines and PrECs. ( a ) Principal Component Analysis (PCA) of the RNA-Seq data for all the clones and PrEC. ( b ) Prostate tissue UMAP plots obtained using scRNA-Seq by the Human Protein Atlas (with superimposed expression of Actin (ACTG1)) identify all distinct populations in the primary human prostate . ( c ) Gene expression heat map of predicted correlation scores (Preds) of each clone and hPrECs to the cell populations identified in the human prostate using scRNA-Seq. Prediction scores range from 0.0 to 1.0 (blue to dark red scale on the left). The distinct cell populations identified by the Human Atlas using single cell-RNA-Seq are labeled by color and a number (top of the heatmap and legend on the right). Clones and PrEC RNA-Seq samples were analyzed in triplicate. The prediction score in B indicate that the clones are most closely related to the basal prostatic population designated c2 (labeled red/orange in the first column of the heat map).

Article Snippet: Fig. 6 RNA-Seq Analysis showing gene expression and clustering of the immortalized cell lines and PrECs. ( a ) Principal Component Analysis (PCA) of the RNA-Seq data for all the clones and PrEC. ( b ) Prostate tissue UMAP plots obtained using scRNA-Seq by the Human Protein Atlas (with superimposed expression of Actin (ACTG1)) identify all distinct populations in the primary human prostate . ( c ) Gene expression heat map of predicted correlation scores (Preds) of each clone and hPrECs to the cell populations identified in the human prostate using scRNA-Seq.

Techniques: RNA Sequencing, Gene Expression, Clone Assay, Expressing, Labeling