Sunday, 7 February 2016

Our first paper on the bioRxiv

I just uploaded our paper, which has also been submitted to BioTechniques, onto the bioRxiv preprint server. The work we present comes from an idea I had shortly after first using Agilent's BioAnalyser in 2000. I was blown away by this piece of technology that has become the de facto standard for RNA QC, and has also pretty much replaced gel electrophoresis for DNA fragment analysis in NGS applications. When launched in 1999, it was the only microfulidics instrument for biology applications. The idea was a simple one: can bioanalyser chips be swapped between assays?


Figure 1: qualitative analysis of the same sample across different chips


In Bioanalyzer chips can be used interchangeably for many analyses of DNA or RNA we show that for RNA and NGS library size they most certainly can. We evaluated the compatibility of two of the most commonly used BioAnalyser kits (RNA6000 and DNA-HS) with three BioAnalyser chip types (RNA6000, DNA1000 and DNA-HS). Importantly, the sticker displaying the chip layout was disregarded and the loading pattern indicated in the assay-specific protocol was used in each experiment. Concentration and RIN of each RNA sample were highly comparable within and between chips, and well within the normal variability expected of samples submitted for RNA-seq experiments. For NGS libraries the average size estimated across all Bioanalyzer chips was 290bp with a 40bp range across all samples, while DNA concentration showed a 10-20% variation in concentration across chips.
Although the quantitative analysis of DNA (NGS libraries) was not so great  we'd always recommend quantitative PCR. Our quantitative results appear to be due to higher variability for concentration data between chip types, although this was due to inter-chip variability and not due to chip type. I've never been a fan of using the BioAnalyser for quantitative analysis, except perhaps in RNA-seq or microarrays where the amount of RNA being used is often less critical. 
Jess and Tom did the work in the lab and drafted the manuscript. This paper has been long in the making. Although the idea is nearly twenty years old it was "sat on the back boiler" for a long time while other more important work got done. In the end it was only a few days of lab work and we spent more time in the writing and correspondence than Jess or Tom spent in the lab. BioTechniques may only have an impact factor of 3 compared to Nature Methods 30, but it is a well respected journal that publishes lots of very useful articles. It is one of the journals I have read the longest and still puts out lots of great work.

bioRxiv: I've never put a paper up on the bioRxiv before but am a fan of the philosophy (although it is not the perfect publication platform). The University of Cambridge encourages work to be published in open-access format and I hope this will help get the work into the hands of people who want to read it. Our posting on bioRxiv is an extra push to make our data, and conclusions, freely available. We also get a DOI so the work can immediately be cited.
The paper has been published under the most open "CC-BY" license so anyone can share, reuse, remix, or adapt this material for any purpose, providing the original authors are credited and cited. option as the most liberal in terms of re-use, data mining etc.

I'm now waiting for the article screening process on bioRxiv to be completed so I can update the post with the DOI.

8 comments:

  1. It is all about how we interact with the problem. The qualitative article critique give us wide range of research on the same topic.

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  2. This was an amazingly helpful tip as we always seem to have excess RNA chips to use up! I tested this for RNA pico chips and these can also run as a DNA chip following the instructions in this paper. Thanks James!

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