Journal: Disease Models & Mechanisms

Article Title: Molecular Subtyping Resource: a user-friendly tool for rapid biological discovery from transcriptional data

doi: 10.1242/dmm.049257

Figure Lengend Snippet: Data import and exploratory analysis. (A) Two input files are required to begin the analytical pipeline in the app – a gene expression matrix and a metadata that includes sample group labelling. (B) Following data upload, the data summary on samples will be displayed for quick review. (C,D) Exploratory visualisation of data will be provided in a form of 2D principal component analysis (PCA) plot (C) and a 3D PCA plot (D) with labelled sample groups.

Article Snippet: Instructions are displayed on the left-hand side of the plot, under the Plotly mode bar control, and hovering over the 3D PCA graphic itself will also reveal the built-in adjustable options above the sample labels on the top right.

Techniques: Gene Expression

Journal: Nature neuroscience

Article Title: Kcnn2 blockade reverses learning deficits in the mouse model of Fetal Alcohol Spectrum Disorders

doi: 10.1038/s41593-020-0592-z

Figure Lengend Snippet: ( a ) Design of the lineage-tracing HSE-FLPo;FRT-STOP-RFP (HSE-RFP) reporter system. ( b ) Experimental timeline. ( c , d ) RFP reporter expression was observed in a subset of GFP + electroporated neurons in layer III of the M1 in PAE mice, but not in control mice. ***P = 0.0003 by two-tailed Student’s t -test (n = 10 animals per group). In box plots ( d ), the line within the box indicates the median, and the upper and lower edges of the box represent the 25th and 75th percentiles, respectively. The upper and lower whisker boundaries indicate the 10th and 90th percentiles, respectively, and dots indicate outliers. ( e ) Representative images of sampling intracellular contents from a single cell (time course, top to bottom). Similar results were obtained with n = 4 animals. ( f ) Principal Component Analysis shows highly variable molecular properties of reporter + neurons in PAE mice (red), segregated from the clusters of reporter − neurons in PAE (green) and control (blue) mice, and the cluster of olfactory bulb (OB) neurons (black) [olfactory bulb neurons: n = 4, reporter + neurons (PAE): n = 15, reporter − neurons (PAE): n= 7, reporter − neurons (control): n = 6]. ( g ) Gene counts against the entropy score among reporter + neurons in PAE mice defined by ROKU. Left and right sides of a broken line include the upregulated and downregulated genes in reporter + neurons, respectively. The genes in yellow bars are considered as specifically changed in reporter + neurons. ( h , i ) K-means clustering and heatmaps of 73 upregulated ( h ) and 20 downregulated ( i ) genes in the reporter + neurons defined by ROKU (in the yellow bars in g ). Gene names (from left to right in h and i ) are re-listed in . Red, green and blue colors in the y-axis correspond to each cell in PCA (see f ).

Article Snippet: A Principal Component Analysis (PCA) plot and hierarchical clustering (with parameters “average” for clustering method and correlation for distance) was generated using Partek.

Techniques: Expressing, Control, Two Tailed Test, Whisker Assay, Sampling

Journal: Metabolites

Article Title: Combined Metabolomics and Biochemical Analyses of Serum and Milk Revealed Parity-Related Metabolic Differences in Sanhe Dairy Cattle

doi: 10.3390/metabo14040227

Figure Lengend Snippet: Multivariate statistical analysis of metabolites identified from Sanhe dairy cattle with 1–4 parities. ( A ) Principal component analysis (PCA) score plot of serum samples from S1 to S4 based on untargeted metabolomics. ( B ) PCA score plot of milk samples from S1 to S4 based on untargeted metabolomics. The abscissa PC1 = first principal component and the ordinate PC2 = second principal component.

Article Snippet: The PCA score plots ( A) of the serum samples from Sanhe dairy cattle revealed distribution between the four parities.

Techniques: