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New technologies allow us to examine the transcriptome at incredible depth and resolution. We have used both genome-scale tiling arrays and new generation massively parallel sequencing to examine the transcriptome of  wild-type C. elegans across development to analyse gene structure and splice variation. We also compared the wild-type transcriptome with that of animals that have lost the nonsense-mediated decay pathway.



We used both genome coverage tiling arrays (Affymetrix) and deep sequencing (Illumina) to characterise the worm transcriptome across development. 

We find that:
  • both sequencing and tiling give very similar views of the transcriptome (see Fig1).
  • ~5% of all transcribed regions identified are novel
  • at least 5% of genes change isoforms across development we detect these changes both from tiling and seq data (see Fig 2)



These data provide a deep, high resolution view of the normal transcriptome — we can use this to investigate how this is perturbed in mutants (e.g. splice factor mutants).