Figure 2.
Global gene expression profiling of LCs and SVECs. (A) The GEA values and heat maps of selected genes obtained from GEXC analysis. The GEA values are listed in the data tables to the left of the heat maps. Magenta, high expression; white, threshold level expression; blue, low expression. GEA values are percentile ranks comparing the expression intensity in the data sets to the common reference of pooled human microarray data from various cell types and tissues (see supplemental Data for more information). (B) A diagram of the percentage of similarly expressed genes between LCs and SVECs. (C) Pearson correlation coefficient (r) by GEA between LCs and SVECs obtained from GEXC analysis. r value was calculated according to biological replicates of microarrays from 3 different normal spleen samples. (D) The heat map of relative expression intensity of LC-SVEC specific genes detected by 341 probes selected using stringent criteria. Selected downregulated genes and the top 20 upregulated genes are listed at the side. (E) The heat map of relative gene expression intensity for LC-SVEC gene signature containing differentially expressed genes detected by 2345 probes. (F) DAVID Functional Annotation Clustering of genes in LC-SVEC gene signature. Downregulated genes in LCs involving blood vessel formation, cell proliferation, and cell migration and intercellular and cell–extracellular matrix interaction (i); upregulated genes in LCs involving endocytosis, and intracellular transportation and iron transportation (ii); differentially expressed cell skeleton genes and genes in Rho GTPase signaling pathway (iii). (G,I) The GEA values (as described in Figure 2A) of genes involved in phagocytosis and genes encoding macrophage/monocyte antigens (G), and genes encoding Rho GTPase signaling pathway members (I). (H,J) RT-qPCR analysis of TFRC (transferrin receptor), MRC1 (CD206), and STAB2 (Stabilin-2) (H); RHOU (J). The expression of all genes was normalized to GAPDH, and the relative expression of a LC gene was calculated against that of SVEC, which was set as 1. Expression of housekeeping gene HPRT was included in each plot as a control. Data are shown as mean ± standard deviation (SD) of triplicate analyses.

Global gene expression profiling of LCs and SVECs. (A) The GEA values and heat maps of selected genes obtained from GEXC analysis. The GEA values are listed in the data tables to the left of the heat maps. Magenta, high expression; white, threshold level expression; blue, low expression. GEA values are percentile ranks comparing the expression intensity in the data sets to the common reference of pooled human microarray data from various cell types and tissues (see supplemental Data for more information). (B) A diagram of the percentage of similarly expressed genes between LCs and SVECs. (C) Pearson correlation coefficient (r) by GEA between LCs and SVECs obtained from GEXC analysis. r value was calculated according to biological replicates of microarrays from 3 different normal spleen samples. (D) The heat map of relative expression intensity of LC-SVEC specific genes detected by 341 probes selected using stringent criteria. Selected downregulated genes and the top 20 upregulated genes are listed at the side. (E) The heat map of relative gene expression intensity for LC-SVEC gene signature containing differentially expressed genes detected by 2345 probes. (F) DAVID Functional Annotation Clustering of genes in LC-SVEC gene signature. Downregulated genes in LCs involving blood vessel formation, cell proliferation, and cell migration and intercellular and cell–extracellular matrix interaction (i); upregulated genes in LCs involving endocytosis, and intracellular transportation and iron transportation (ii); differentially expressed cell skeleton genes and genes in Rho GTPase signaling pathway (iii). (G,I) The GEA values (as described in Figure 2A) of genes involved in phagocytosis and genes encoding macrophage/monocyte antigens (G), and genes encoding Rho GTPase signaling pathway members (I). (H,J) RT-qPCR analysis of TFRC (transferrin receptor), MRC1 (CD206), and STAB2 (Stabilin-2) (H); RHOU (J). The expression of all genes was normalized to GAPDH, and the relative expression of a LC gene was calculated against that of SVEC, which was set as 1. Expression of housekeeping gene HPRT was included in each plot as a control. Data are shown as mean ± standard deviation (SD) of triplicate analyses.

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