Can anyone recommend the best equipment, tools or protocols -- in plants with incipient genome sequencing, or even in well defined genome sequences?
Thanks Ivan, but I am rather active in metabolomics, not in transcriptomics...
Illumina seems to be the most widespread platforms, and the cheapest. Transcriptomics based on Next Generation Sequencing technology is used especially for organisms with an entirely published and annotated genome, such as Arabidopsis, tomato, grape, ecc. These few words are not exhaustive about the topic, because the rapidly increasing of literature on it.
Has anyone used Ion torrent for an Arabidopsis transcriptome? Is the yield enough? Thanks!
Actually, you are right. However, manipulation of RNA-Seq data of annotated genome yield more informative results. Finally, your comment is pertinent, thanks.
For species without the annotated genomes you can try the transcriptome de-novo assembly, proper RNAseq would not work - requires a reference genome and its annotation. De novo transcriptome will give you contig-isotig-isogroup (i.e sort of exon-transcript-group of transcripts) bundles.
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