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. Author manuscript; available in PMC: 2011 Jul 29.

Published in final edited form as: Nat Biotechnol. 2010 May 2;28(5):511–515. doi: 10.1038/nbt.1621

Excluding isoforms discovered by Cufflinks from the transcript abundance estimation impacts the abundance estimates of known isoforms, in some cases by orders of magnitude. Four-and-a-half-LIM domains 3 (Fhl3) inhibits myogenesis by binding MyoD and attenuating its transcriptional activity. (a) The C2C12 transcriptome contains a novel isoform that is dominant during proliferation. The new TSS for Fhl3 is supported by proximal TAF1 and RNA polymerase II ChIP-Seq peaks. (b) The known isoform (solid line) is preferred at time points following differentiation.

Excluding isoforms discovered by Cufflinks from the transcript abundance estimation impacts the abundance estimates of known isoforms, in some cases by orders of magnitude. Four-and-a-half-LIM domains 3 (Fhl3) inhibits myogenesis by binding MyoD and attenuating its transcriptional activity. (a) The C2C12 transcriptome contains a novel isoform that is dominant during proliferation. The new TSS for Fhl3 is supported by proximal TAF1 and RNA polymerase II ChIP-Seq peaks. (b) The known isoform (solid line) is preferred at time points following differentiation.