Skip to main content
. Author manuscript; available in PMC: 2018 Dec 25.
Published in final edited form as: Nat Microbiol. 2018 Jun 25;3(7):814–823. doi: 10.1038/s41564-018-0177-8

Figure 4. Transcriptome analysis of host epithelia and C. parvum.

Figure 4

(a) Volcano plot showing differential expression of host genes between oocyst- and media (control)-injected organoids at 24 and 72 hr post-injection (n=3 biologically independent samples). Each dot represents a gene. The red and green dots represent differentially expressed genes with p-value < 0.05 and with p-value <0.1 (Wald test), respectively upon injection. The vertical lines represent log2 fold change values as indicated in x axis. List of differentially expressed genes are available in Supplementary Table 1.

(b) Heatmap showing the expression of top 30 induced genes in lung organoids at 24 hr post-injection (n=3 biologically independent samples). Expression values are expressed as Z-score transformed transcript count.

(c) (top) Heatmap showing the expression of 30 induced genes in lung organoids at 72 hr post-inject (n=3 biologically independent samples). (bottom) Gene set enrichment assay (GSEA) plot showing strong enrichment of type I interferon regulation genes in oocyst-injected lung organoids. NES: normalized enrichment score, p-value is nominal p-value. Black bars underneath the graph present the rank position of genes from the gene set. GSEA plots of genes in differentiated SI organoids are available in Supplementary Fig. 5.

(d) Volcano plot showing differential expression of C. parvum genes between 24 and 72 hr post-injection into differentiated SI and lung organoids (n=3 biologically independent samples). The magenta and blue dots indicate enriched genes with p-value <0.05 and with p-value <0.1 (Wald test), respectively. List and GO-term analysis of differentially expressed C. parvum genes are available in Supplementary Table 2 and Fig 6, respectively.

(e) Heatmap showing the expression of ribosomal protein coding genes (top) and oocyst wall protein genes (bottom) of C. parvum in lung organoids at 24 and 72 hr post-injection (n=3 biologically independent samples). Heatmap of C. parvum genes in SI organoids are available in Supplementary Fig. 7.