The porcine piRNA transcriptome response to Senecavirus a infection

Figures

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  Figure 1. (A) Length distribution of PIWI-interacting RNAs (piRNAs). (B) First base preference of different length piRNAs. (C) Unique piRNA and piRNA source distribution. (D) piRNA chromosome density map.

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  Figure 2. Heat map and hierarchical clustering of miRNA high-throughput sequencing data. Heat mapping and hierarchical clustering was used to analysis the PIWI-interacting RNA (piRNA) high-throughput sequencing data of non-infected and SVA-infected PK-15 cells based on their expression level. (A) piRNA heat map. (B) piRNA cluster heat map. The grey line indicates high relative expression, and the blue line indicates low relative expression.

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  Figure 3. Volcano map of PIWI-interacting RNA (piRNA) high-throughput sequencing data. (A) Volcano map of piRNA expression between non-infected and SVA-infected PK-15 cells. (B) Volcano map showing variations in piRNA cluster expression between non-infected and SVA-infected PK-15 cells. The high-throughput sequencing data are graphed on a volcano map to visualize variations in piRNA expression. The values on the X and Y axes of the scatter plot are the normalized signal values for the samples (log2 scaled). The dashed lines are fold-change lines (the default fold-change value is 2.0). The expression of piRNA on the left side of the left dashed line or on the right side of the right dashed line was more than two-fold different.

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  Figure 4. PIWI-interacting RNA (piRNA) differential expression analysis. (A) Venn diagram showing the distribution of 3,608 unique piRNAs between non-infected PK-15 cells and SVA-infected PK-15 cells. A total of 173 piRNAs with DE were identified in SVA-infected PK-15 cells. (B) Venn diagram showing the distribution of 225 piRNA clusters between non-infected and SVA-infected PK-15 cells. A total of 60 piRNA clusters with DE were identified in SVA-infected PK-15 cells.

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  Figure 5. Comparison of qRT-PCR and high-throughput sequencing results.

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  Figure 6. Gene ontology (GO) annotation of piRNA target genes. (A) GO annotation of differentially expressed piRNA target genes in SVA-infected PK-15 cells (vs. non-infected PK-15 cells). (B) Scatter plot of candidate target gene KEGG enrichment. The vertical axis represents the pathway name, horizontal axis represents the rich factor, size of the dot indicates the number of candidate target genes in this pathway, and color of the dot corresponds to different Q-value ranges. (C) Transcriptional level of BMAL1 was detected by qRT-PCR. (D) Transcriptional level of CRY1 was detected by qRT-PCR.