GSE40180

Overall design: CPL-injured MSC samples vs. Control (subtract overlapping CPL-injured + Placebo vs Control) for each tissue.

Efferocytosis

Spleen MSC vs Control

Liver MSC vs Control

Heart MSC vs. Control

Kidney MSC vs Control

Lung MSC vs Control

Common MSC stimulated genes across tissues

Note: this is a microarray probe set, multiple probes per gene transcript. Best practice to test probes for DE independently, loss of information if averaging expression

  • ILMN_2488343: Wdfy3
  • ILMN_2826414: Wdfy3
  • ILMN_2946088: Panx1
  • ILMN_2647544: Panx1
# Panx1 , Wdfy3
probe_ids <- c("ILMN_2488343", "ILMN_2826414", "ILMN_2946088", "ILMN_2647544")
cts <- counts
colnames(cts) <- pheno[colnames(cts), "status"]
cts <- cts[probe_ids,]
cts <- cts[, c(1:4, 10:14, 20:24, 49:52, 58:62, 68:72)]

cts <- t(cts)
cts <- scale(cts, center=T, scale = T)
cts <- t(cts)

annot_col <- data.frame(row.names = colnames(cts), status = factor(c(rep(c(rep("Spleen", 4), rep("Heart", 5), rep("Lung", 5)), 2))))

cols <- c("blue", "red", "gold2")
names(cols) <- c("Spleen", "Heart", "Lung")
annot_colors <- list(status = cols)

library(viridis)
## Loading required package: viridisLite
pheatmap::pheatmap(cts, cluster_cols = F, cluster_rows = T, show_rownames = T,
                   show_colnames = T, annotation_col = annot_col,
                   annotation_colors = annot_colors,
                   col = hcl.colors(100, "Purple-Green",rev=F),
                   main = "DE Efferocytosis Wdfy3, Panx1 Heart, Lung\nP.Value <= 0.05",
                   cutree_cols = 2)

Fibrosis

Spleen MSC vs Control

Liver MSC vs Control

Heart MSC vs. Control

Kidney MSC vs Control

Lung MSC vs Control