heatmaps and as box-and-whisker plots  (GraphPad Software Inc)

Journal: Nature Communications

Article Title: Natural variation of an E3 ubiquitin ligase encoding gene Chalk9 regulates grain chalkiness in rice

doi: 10.1038/s41467-025-61683-4

Figure Lengend Snippet: a The genome-wide association signals for chalky grain rate (CGR) and degree of chalkiness (DC) in the region at 18–21 Mb on chromosome 9 ( x -axis) across two years. Negative log 10 -transformed P values from the linear mixed model are plotted on the y -axis. The horizontal dashed line indicates the genome-wide significance threshold ( P = 1×10 –6 ). P values were determined using a two-sided Wald test and assessed after Bonferroni correction for multiple comparisons. b Linkage disequilibrium (LD) heatmap of the Chalk9 locus region. Pairwise linkage disequilibrium was determined by calculating r 2 (the square of the correlation coefficient between SNPs). c Relative expression level of the 12 candidate genes in the endosperm of eight high-chalky and eight low-chalky varieties at 20 days after flowering (DAF). The 12 predicted genes in the Chalk9 locus region are labeled by I to XII. Data show means ± SD ( n = 8 varieties). P values were calculated for comparisons between high-chalky and low-chalky groups, with each group comprising 8 varieties. d Relative expression level of the candidate gene III ( Chalk9 ) in the endosperm from the selected varieties at 20 DAF. The P value was calculated for the comparison between high-chalky and low-chalky groups, with each group comprising 8 varieties. Data show means ± SD ( n = 3 biological replicates). e Relative expression level of the 12 candidate genes in the leaves of eight high-chalky and eight low-chalky varieties. Data show means ± SD ( n = 8 varieties). In c – e , statistical analysis between high-chalky and low-chalky groups was performed by two-tailed Student’s t -test. Source data are provided as a Source Data file.

Article Snippet: Correlation analysis, heatmap plotting, and volcano plot analysis were performed using BMKCloud ( www.biocloud.net ).

Techniques: GWAS, Transformation Assay, Genome Wide, Expressing, Labeling, Comparison, Two Tailed Test

Journal: bioRxiv

Article Title: The mitochondrial NAD transporter SLC25A51 is a modulator of beta cell senescence and type 2 diabetes

doi: 10.1101/2025.04.09.647991

Figure Lengend Snippet: (A) ( A ) A diagram depicting the generation of SLC25A51-floxed C57BL/6N mice using a CRISPR-Cas9-based approach by Biocytogen Pharmaceuticals. ( B, C ) SLC25A51 expression per cell was compared between T2D patients and healthy controls using two different human beta-cell scRNA-seq datasets (E-MTAB-5061, GSE81608) ( Table S3 ). Heatmaps of Cdkn1a (p21) and Cdkn2a (p16) expression were also analyzed in both datasets. ( D ) 30-week-old SLC25A51-floxed C57BL/6N male mice were infused with either AAV6-INS1-Empty or AAV6-INS1-CRE viruses via pancreatic ductal infusion. Mice were sacrificed 15 weeks post-surgery. SLC25A51, p16 INK4A , MTCO2, and beta-actin protein expression levels were analyzed in pancreatic beta cells isolated from 45-week-old INS1-EMPTY (n=2) and INS1-CRE (n=4) groups. ( E-K ) Pancreatic ductal infusion of either PBS, AAV6-INS1-Empty, or AAV6-INS1-CRE was performed in each group of female C57BL/6N mice (n=5–6 per group). ( F ) Random blood glucose levels and ( G ) body weight were measured twice a week, and ( H ) beta-hydroxybutyrate levels were measured once a week for each mouse. ( I-K ) Six or eight weeks post-surgery, female mice underwent an IPGTT and ITT. Graphs show blood glucose levels at ( I, J ) each time point and area under the curve. ( I ) During the IPGTT, serum was collected from each group at 0 and 15 min to measure ( K ) serum insulin levels. Two weeks after the IPGTT, ( J ) an ITT was performed to test insulin sensitivity. Two-way ANOVA; error bars represent SEM; **p < 0.01.

Article Snippet: The data were visualized using heatmaps or dot-plot graphs in GraphPad Prism.

Techniques: CRISPR, Expressing, Isolation