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Differential Gene Expression in the Siphonophore Nanomia bijuga (Cnidaria) Assessed with Multiple Next-Generation Sequencing Workflows

Figure 2

Physical distribution of mapped short-read sequences across an example transcript.

Read distribution is shown for a fibrillar collagen (isogroup06489, tblastx e-value 1e-87) for the three nectophore samples. Gastrozooid expression was much lower and not visible on the same scale. All three short-read workflows found significant differential expression for this gene. The gene is drawn in the 5′–3′ direction (4,864 bp). Height of the colored bars indicates the number of reads mapped to that location. Count data are not normalized, so differences in amplitude across samples can be due to differences in sequencing effort across samples. Reads above the line map in the sense direction, below the line in the antisense direction. Helicos DGE reads (red) are sense and unexpectedly tended to map to the 3′ end. Illumina mRNA-Seq reads (green) map to sense and antisense strand along the whole gene. The largest stack of reads for SOliD SAGE (blue) is adjacent to the 3′-most NlaIII cutting site.

Figure 2