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(A ) RPKM values of reads uniquely mapped to either 5′ UTR or CDS of transcripts (same list of transcripts as in Figure 1 source data 1 ).

While on one hand, PHA-4 transcriptionally upregulates the expression of a many transcripts, the same set of transcripts are potentially targeted by miRNAs that it transcribes.

For each transcript, the same number of reads as in the template data set was generated by the simulator.

The tdnaΔ strains showed a longer ∼1200-base ∼1200-base, transcriptengtheasameen using the ATG31 coding-sequence probe.

Two transcripts with same TSS were considered as the same transcript and TPs composed of such transcripts were discarded.

When the analysis was restricted to defense-related transcripts the same broad trend was observed.

All the transcripts for a particular gene were grouped into clusters of transcripts with the same transcription start site (TSS).

If multiple Affymetrix probe sets were linked to the same transcript, the maximally regulated transcript was chosen.

These two probes were designed from the same transcript, however two other transcripts from the same gene had significant signal intensities.

Of the 1,745 catfish gene transcripts, 416 transcripts shared the same gene identity between blue catfish and channel catfish.

To prevent double counting of poly(A) sites corresponding to multiple transcripts from the same gene, multiple transcripts from the same gene were merged into one unique gene model.