pca plot generation  (GraphPad Software Inc)

Journal: Cytotherapy

Article Title: Characterizing human mesenchymal stromal cells’ immune-modulatory potency using targeted lipidomic profiling of sphingolipids

doi: 10.1016/j.jcyt.2021.12.009

Figure Lengend Snippet: Unstimulated and IFN-γ–stimulated BM-MSC SL profile. (A) Schematic illustrating IDO converting tryptophan to kynurenine (kyn), an immunosuppressive metabolite. (B) SL concentrations of unstimulated and IFN-γ–primed MSCs. (C) PCA of high and low IDO unstimulated (Unstim) MSC groups. (D) PCA variable plot of MSC groups. (E) PCA of high and low IDO IFN-γ–primed groups. (F) PCA variable plot of IFN-γ groups. (G) LDA of high and low MSCs from Unstim and IFN-γ groups. *Statistical significance (P < .05). Mann–Whitney U test was used to determine significance. All groups were measured in triplicates (n = 3).

Article Snippet: Graphical illustrations of PCA variable loading plots were generated in RStudio.

Techniques: MANN-WHITNEY

Journal: Frontiers in Immunology

Article Title: TLR3 Signaling Promotes the Induction of Unique Human BDCA-3 Dendritic Cell Populations

doi: 10.3389/fimmu.2016.00088

Figure Lengend Snippet: Poly I:C-stimulated ILT4 − and ILT4 + BDCA-3 cDCs have unique cytokine and gene signatures . (A) Experimental design of BDCA-3 DC phenotyping. (B) BDCA-3 cDCs were cultured with Poly I:C for 18 h and then sorted into ILT4 − and ILT4 + populations. Cells were then plated without further stimulation for 18 h. Supernatants were assayed for cytokine and chemokine content by luminex analysis. P -values generated using two-tailed student’s paired t -test (95% confidence interval). Graphs represent four donors. (C) BDCA-3 cDCs were stimulated with Poly I:C for 18 h, Golgistop was then added for 6 h. Cells were surface stained with ILT3, ILT4, and CD141 and then intracellularly stained with IFN-γ and TNF-α. Data showing intracellular staining are representative of one donor out of four. (D) Genomic profiling of ILT4 − vs. ILT4 + was performed using GeneChip Human Gene 1.0 ST arrays. Principal component analysis (PCA) was computed using OmicSoft ArrayStudio, and a plot was generated to show the relative clustering of ILT4 − and ILT4 + . ILT4 − and ILT4 + populations were compared to each other by t -test with a threshold set for a fold change >1.5 and a P -value <0.05. ILT4 gene expression was confirmed by qPCR. (Data shown are one representative donor out of four).

Article Snippet: A 3D plot generated by PCA with OmicSoft ArrayStudio across all probe sets revealed that ILT4 + cells are most dissimilar from ILT4 − cells (Figure D).

Techniques: Cell Culture, Luminex, Generated, Two Tailed Test, Staining, Gene Expression