Additional file 12.

Visualization of transcripts exhibiting 3' decay in poly(A)- samples. (a) Examples of 3' decay in the bimorphic group. pdk 4 (pyruvate dehydrogenase kinase, isozyme 4) is expressed in HeLa cells only and shows similar normalized read densities in poly(A)+ and poly(A)- samples; however, it exhibits a gradual decay pattern (blue dashed lines) from 3' to 5' in the poly(A)- sample in HeLa cells. (b-d) Examples of 3' decay in the poly(A)+ group. Note that sfrs18 (splicing factor, arginine/serine-rich 18), sf3b2 (splicing factor 3b, subunit 2) and eif3a (eukaryotic translation initiation factor 3) all exhibit a gradual decay pattern (blue dashed lines) from the 3' to 5' ends in poly(A)- samples in both H9 and HeLa cells, although both are more abundant in poly(A)+ samples. See text for details.

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Yang et al. Genome Biology 2011 12:R16   doi:10.1186/gb-2011-12-2-r16