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

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1 Graduate Program in Biophysics, University of California, Berkeley, CA, United States
2 Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
3 Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
DOI
10.7287/peerj.preprints.779v1
Published
Accepted
Subject Areas
Bioinformatics, Biotechnology, Computational Biology, Genomics
Keywords
RNAseq, single cell, protocols, linear output
Copyright
© 2015 Combs et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
Cite this article
Combs PA, Eisen MB. 2015. Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols. PeerJ PrePrints 3:e779v1

Abstract

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 metrics of interest to us than a more standard protocol, 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.

Author Comment

This is a submission to PeerJ for review.