Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols

PeerJ. 2015 Mar 26;3:e869. doi: 10.7717/peerj.869. eCollection 2015.


Recently, a number of protocols extending RNA-sequencing to the single-cell regime have been published. However, we were concerned that the additional steps to deal with such minute quantities of input sample would introduce serious biases that would make analysis of the data using existing approaches invalid. In this study, we performed a critical evaluation of several of these low-volume RNA-seq protocols, and found that they performed slightly less well in per-gene linearity of response, but with at least two orders of magnitude less sample required. We also explored a simple modification to one of these protocols that, for many samples, reduced the cost of library preparation to approximately $20/sample.

Keywords: Linear output; Protocols; RNAseq; Single cell.

Grant support

This work was funded by a Howard Hughes Medical Institute investigator award to Michael B. Eisen, and National Institutes of Health training grant #T32 HG 00047 to PAC. This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 Instrumentation Grants S10RR029668 and S10RR027303. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.