Platform evaluation project

In WP3 (a working package to develop new technologies, lead by Piero), a variety of transcriptome profiling methodology have been developed and discussed. While HeliScopeCAGE will be the protocol to profile the widest range of samples in FANTOM5, we are also thinking to use other protocols, such as nanoCAGE, solexa/taggingCAGE, RNA-seq, ...etc in a complemental manner. It is essential to know their consistencies and performance on a unified ground for this purpose.

We set up a 'platform evaluation project' to apply the selected protocols on the same pools of RNAs with technical replicates. We also profiled the same RNAs with microarray and qRT-PCR to compare the developed method to conventional technologies.

The RNA pools used here:

• RA: THP-1 100% / HeLa 0%
• RB: THP-1 99% / HeLa 1% mix
• RC: THP-1 95% / HeLa 5% mix
• RD: THP-1 90% / HeLa 10% mix
• RE: THP-1 50% / HeLa 50% mix
• RF: THP-1 0% / HeLa 100%

The protocols in our scope are:

• HeliScopeCAGE (manual standard version) - HeliScopeCAGE
• nanoCAGE
• Illumina/taggingCAGE
• RNA-seq
• small RNA

Visualization of the preliminary data:

• Basic config for the technology evaluation (RA~RF) EvaluationCAGE
• Basic config for short RNA technology evaluation (RA~RF)EvaluationShortRNA

Kawaji is taking care of this project, with Piero, Al, and the developers of each technologies, and I am also analyzing the obtained data with Marina. We hope to share the results with the consortium soon (hopefully). If any of you are very interested in this data and hope to see some more preliminary results, please contact kawaji@gsc.riken.jp