Evaluation of commercially available RNA amplification kits for RNA sequencing using very low input amounts of total RNA

Savita Shanker, Ariel Paulson, Howard J. Edenberg, Allison Peak, Anoja Perera, Yuriy O. Alekseyev, Nicholas Beckloff, Nathan J. Bivens, Robert Donnelly, Allison F. Gillaspy, Deborah Grove, Weikuan Gu, Nadereh Jafari, Joanna S. Kerley-Hamilton, Robert H. Lyons, Clifford G Tepper, Charles M. Nicolet

Research output: Contribution to journalArticle

24 Scopus citations

Abstract

This article includes supplemental data. Please visit http://www.fasebj.org to obtain this information.Multiple recent publications on RNA sequencing (RNA-seq) have demonstrated the power of next-generation sequencing technologies in whole-transcriptome analysis. Vendor-specific protocols used for RNA library construction often require at least 100 ng total RNA. However, under certain conditions, much less RNA is available for library construction. In these cases, effective transcriptome profiling requires amplification of subnanogram amounts of RNA. Several commercial RNA amplification kits are available for amplification prior to library construction for next-generation sequencing, but these kits have not been comprehensively field evaluated for accuracy and performance of RNA-seq for picogram amounts of RNA. To address this, 4 types of amplification kits were tested with 3 different concentrations, from 5 ng to 50 pg, of a commercially available RNA. Kits were tested at multiple sites to assess reproducibility and ease of use. The human total reference RNA used was spiked with a control pool of RNA molecules in order to further evaluate quantitative recovery of input material. Additional control data sets were generated from libraries constructed following polyA selection or ribosomal depletion using established kits and protocols. cDNA was collected from the different sites, and libraries were synthesized at a single site using established protocols. Sequencing runs were carried out on the Illumina platform. Numerous metrics were compared among the kits and dilutions used. Overall, no single kit appeared to meet all the challenges of small input material. However, it is encouraging that excellent data can be recovered with even the 50 pg input total RNA.

Original languageEnglish (US)
Pages (from-to)4-18
Number of pages15
JournalJournal of Biomolecular Techniques
Volume26
Issue number1
StatePublished - 2015

Keywords

  • CDNA synthesis kits
  • PolyA
  • Ribodepletion

ASJC Scopus subject areas

  • Molecular Biology

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    Shanker, S., Paulson, A., Edenberg, H. J., Peak, A., Perera, A., Alekseyev, Y. O., Beckloff, N., Bivens, N. J., Donnelly, R., Gillaspy, A. F., Grove, D., Gu, W., Jafari, N., Kerley-Hamilton, J. S., Lyons, R. H., Tepper, C. G., & Nicolet, C. M. (2015). Evaluation of commercially available RNA amplification kits for RNA sequencing using very low input amounts of total RNA. Journal of Biomolecular Techniques, 26(1), 4-18.