Journal: Nature Genetics

Article Title: Multi-omic profiling of clear cell renal cell carcinoma identifies metabolic reprogramming associated with disease progression

doi: 10.1038/s41588-024-01662-5

Figure Lengend Snippet: ( a , b ): Boxplot of ( a ) T ex score calculated by ssGSEA algorithm in TJ-RCC tumors and ( b ) proportion of T ex in total T cells in snRNA data. P values were calculated by two-sided Turkey’s test. IM1: n = 22, IM2: n = 27, IM3: n = 36, IM4: n = 15. In boxplots, the central line represents the median value, box limits indicate the interquartile ranges, and the whiskers extend to 1.5 times the interquartile range. ( c ): Heatmap showing difference in pathway scores calculated by ssGSEA per cell between different macrophage sub-clusters. Shown are t-values from a lineal model of Limma via comparing selected subgroups to all the other samples. ( d ): Pearson’s correlation between specific subpopulations. P-values are from two-sided Student’s t test. Cell abundance was estimated by ssGSEA score in each sample of TJ-RCC cohort. The red line shows the linear interpolation of the data. X-axes and Y-axes represent ssGSEA score of specific cell types. ( e ): Boxplot of fibroblast score calculated by ssGSEA algorithm in TJ-RCC tumors. P values were calculated by two-sided Tukey’s test. IM1: n = 22, IM2: n = 27, IM3: n = 36, IM4: n = 15. The central line of the box represents the median value, box limits indicate the interquartile ranges, and the whiskers extend to 1.5 times the interquartile range. ( f ): Heatmap showing Pearson’s correlation between cell abundance in TJ-RCC. Cell abundance was represented by ssGSEA score calculated using marker genes from snRNA-seq. ( g ): Ideogram of histological locations of given cell types. ( h ): IHC staining of DCN and ACTA2 on W5_T. Experiment has been repeated three times. ( i ): Multi-color fluorescence on W5_T, associated to Fig. . White box marks a region lack of fibroblast, while yellow box marks a fibroblast enriched region. Figure magnified the yellow box region. ( j ): Multi-color fluorescence on W5_T. Experiment has been repeated three times. ( k ): IHC staining on W5_T. GJA5 marked arterial vascular. Experiment has been repeated three times.

Article Snippet: The following antibodies were used: anti-human CD8 (Abcam, ab178089; 1:100), anti-human CD31 (Proteintech, 11265-1-AP; 1:2,000), anti-Human DCN (Abcam, ab277636, 1:2,000), anti-human CD3 (Proteintech, 17617-1-AP; 1:1,000), anti-human CD163 (Proteintech, 16646-1-AP, 1:2,000), anti-human CX40 (Bioss, bs-1050R; 1:500) and anti-human a-SMA/ACTA2 (Proteintech, 14395-1-AP; 1:2500).

Techniques: Marker, Immunohistochemistry, Fluorescence

Journal: Frontiers in Physiology

Article Title: Low-Level Vagus Nerve Stimulation Reverses Obstructive Sleep Apnea-Related Atrial Fibrillation by Ameliorating Sympathetic Hyperactivity and Atrial Myocyte Injury

doi: 10.3389/fphys.2020.620655

Figure Lengend Snippet: (A) Representative examples of SNRT in the OSA group at baseline, the 1st hour, the 2nd hour, the 3rd hour, the 4th hour, and the 6th hour. (B) Changes in SNRT between the OSA and OSA+LLVS groups at each hour. (C) Changes in ion channels via gene expression level among the three groups. (D) Representative immunohistochemical staining of Cx 40 and Cx 43 on the LA among the three groups. (E) Quantitative analysis of Cx 43 and Cx 40-positive cells in the LA of each group. * p <0.05, ** p <0.01 vs. the control group; # p <0.05, ## p <0.01 vs. the OSA+LLVS group; SNRT, sinoatrial node recovery time; Cx 43, connexin 43; Cx40, connexin 40; H, hours.

Article Snippet: Connexin-40 (Cx40, LS-B959, 1:100, LifeSpan BioSciences, Seattle, WA, United States), and connexin-43 (Cx43, LS-B9771, 1:100, LifeSpan BioSciences, Seattle, WA, United States) were also detected, with quantitative analysis of integrated optical density (IOD) also conducted.

Techniques: Expressing, Immunohistochemical staining, Staining