title: Quantitative transcriptomics using designed primer-based amplification.
abstract: We developed a novel Designed Primer-based RNA-sequencing strategy (DP-seq) that uses a defined set of heptamer primers to amplify the majority of expressed transcripts from limiting amounts of mRNA, while preserving their relative abundance. Our strategy reproducibly yielded high levels of amplification from as low as 50 picograms of mRNA while offering a dynamic range of over five orders of magnitude in RNA concentrations. We also demonstrated the potential of DP-seq to selectively suppress the amplification of the highly expressing ribosomal transcripts by more than 70% in our sequencing library. Using lineage segregation in embryonic stem cell cultures as a model of early mammalian embryogenesis, DP-seq revealed novel sets of low abundant transcripts, some corresponding to the identity of cellular progeny before they arise, reflecting the specification of cell fate prior to actual germ layer segregation.
authors.affiliation: Bioinformatics and Systems Biology Graduate Program, University of California at San Diego, La Jolla, CA, USA.
authors.forename: Vipul
authors.initials: V
authors.lastname: Bhargava
authors.forename: Pang
authors.initials: P
authors.lastname: Ko
authors.forename: Erik
authors.initials: E
authors.lastname: Willems
authors.forename: Mark
authors.initials: M
authors.lastname: Mercola
authors.forename: Shankar
authors.initials: S
authors.lastname: Subramaniam
mesh_terms: D028341:Activins / Q000235:genetics; D000818:Animals; D002478:Cells, Cultured; D017931:DNA Primers; D047108:Embryonic Development / Q000235:genetics; D053595:Embryonic Stem Cells / Q000378:metabolism; D051379:Mice; D016133:Polymerase Chain Reaction / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome; D016212:Transforming Growth Factor beta / Q000235:genetics
chemical_list: D017931:DNA Primers; D012333:RNA, Messenger; D016212:Transforming Growth Factor beta; C422405:activin A; D028341:Activins