Alignment of standard and 3′ RNA-seq data. Percentage alignment is shown against the entire genome (blue bars), against regions of the genomes with annotated features (mRNA, tRNA, rRNA, other known non-coding RNA, orange bars) or against non-feature regions (grey bars). Individual samples are shown on the x-axis with sample groupings indicated above. C = standard RNA-seq samples from fish treated with control conditions, FBSA = standard RNA-seq samples from fish treated with FBSA, LexC = 3′ RNA-seq samples from fish treated with control conditions, LexFBSA = 3′ RNA-seq samples from fish treated with FBSA. Numbers at the end of the sample names indicate biological replicates.

DEG overlap among 3′ and standard RNA-seq. (A) A Venn diagram showing overlap between DEGs identified by the standard RNA-seq approach (blue circle) and DEGs identified by 3′ RNA-seq (red circle). (B) Scatter plot showing the log2 fold change of all 64 DEGs identified by both 3′ and standard RNA-seq. (C) Scatter plot showing the log2 mean expression value of all 64 DEGs identified by both 3′ and standard RNA-seq.

DEG identification with sparse data. (A) The number of genes showing statistically significant increased or decreased expression for standard and 3′ RNA-seq data. (B) The y-axis shows the DEGs identified as data is reduced as a percentage of the DEGs identified with the full dataset. The x-axis shows the percent of full data examined.

Statistical significance and intersection of 3′ and standard RNA-seq enriched functions. For all functions found by both standard and 3′ RNA-seq DEG functional enrichment the −log10 of the q-value is shown. Red bars represent q-values of functions enriched from the 3′ RNA-seq DEG list and blue bars represent functions enriched from the standard RNA-seq DEG list.

Number of enriched functions identified with 3′ and standard RNA-seq DEG lists using sparse data and q-value defined data. (A) Number of enriched functions using DEG lists from 3′ RNA-seq (red bars) and standard RNA-seq (blue bars) data across sparse data sets. Percent of the full data is shown in the x-axis. (B) GSEA analysis of full datasets from standard and 3′ RNA-seq. Venn diagram is shown for functions identified by both approaches (54) with the table below showing the six additional functions identified solely by standard RNA-seq.