Extended Data Fig. 5: Transcriptomic profiling and pathway analysis of B cells populations from FFPE human lymph node. | Nature Methods

Extended Data Fig. 5: Transcriptomic profiling and pathway analysis of B cells populations from FFPE human lymph node.

From: Integration of imaging-based and sequencing-based spatial omics mapping on the same tissue section via DBiTplus

Extended Data Fig. 5: Transcriptomic profiling and pathway analysis of B cells populations from FFPE human lymph node.

a UMAP embedding from DBiTplus following CODEX-guided deconvolution reveals distinct immune and stromal cell populations, including naive B cells, activated B cells, cycling B cells, memory B cells, plasma B cells, and T cell subsets. b Heat map of differentially expressed genes across annotated cell types. c Violin plots of representative (canonical) marker genes for various B cell subtypes. d Volcano plots showing differentially expressed genes in naive (left) and activated (right) B cells compared to all other cells. Differential gene expression computed from two-sided Wilcoxon rank-sum test, adjusted P value on the basis of Bonferroni correction) e Pathway analysis comparing enriched pathways between naïve B cells and activated B cells. f Ingenuity Pathway Analysis (IPA) graphical summary showing predicated canonical pathways, upstream regulators and transcriptional and translational programs in activated B cells.

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