Additional file 3: of Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression

Abstract

Figure S3 DEseq2 analysis of gene expression levels in SOM and IGN. (A) MA plot showing the differential gene expression pattern for SOM and IGN samples. The differentially expressed genes between SOM and IGN were represented with red dots (p adj < 0.01). Y-axis: M (log2TPM (fold change)). X-axis: A (Mean of normalized counts). (B) PCA analysis indicating good correlation between replicates for SOM and IGN samples. (C) Venn diagrams displaying the overlap between Cuffdiff-called and DESeq2-called differentially expressed genes in SOM (top) and IGN (bottom) samples. Of the Cuffdiff-called differentially expressed genes in SOM or IGN, 91.48% or 86.42% were also called by DESeq2, respectively. (D) Boxplot exhibiting the significance of differentially expressed gene sets either called by both Cuffdiff and DESeq2 or DESeq2 only. (E) Boxplot displaying the overall gene expression (TPM) for tissue-enriched transcripts identified by Cuffdiff. Transcripts with less than 10 total read counts across all the samples were removed for TPM analysis. Thus, 3941 out of 3965 SOM-enriched transcripts (blue) or 4940 out of 5075 IGN-enriched transcripts (red) in either SOM RNA-seq or IGN RNA-seq were analyzed. Each box indicates the median and interquartile range of TPM level. (PDF 941 kb