Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers

Responding to change is a fundamental property of life, making time-series data invaluable in biology. For microbes, plate readers are a popular, convenient means to measure growth and also gene expression using fluorescent reporters. Nevertheless, the difficulties of analysing the resulting data can be a bottleneck, particularly when combining measurements from different wells and plates. Here we present omniplate, a Python module that corrects and normalises plate-reader data, estimates growth rates and fluorescence per cell as functions of time, calculates errors, exports in different formats, and enables meta-analysis of multiple plates. The software corrects for autofluorescence, the optical density’s non-linear dependence on the number of cells, and the effects of the media. We use omniplate to measure the Monod relationship for the growth of budding yeast in raffinose, showing that raffinose is a convenient carbon source for controlling growth rates. Using fluorescent tagging, we study yeast’s glucose transport. Our results are consistent with the regulation of the hexose transporter (HXT) genes being approximately bipartite: the medium and high affinity transporters are predominately regulated by both the high affinity glucose sensor Snf3 and the kinase complex SNF1 via the repressors Mth1, Mig1, and Mig2; the low affinity transporters are predominately regulated by the low affinity sensor Rgt2 via the co-repressor Std1. We thus demonstrate that omniplate is a powerful tool for exploiting the advantages offered by time-series data in revealing biological regulation.Author summary: Time series of growth and of gene expression via fluorescent reporters are rich ways to characterise the behaviours of cells. With plate readers, it is straightforward to measure 96 independent time series in a single experiment, with readings taken every 10 minutes and each time series lasting tens of hours. Analysing such data can become challenging, particularly if multiple plate-reader experiments are required to characterise a phenomenon, which then should be analysed simultaneously. Taking advantage of existing packages in Python, we have written code that automates this analysis but yet still allows users to develop custom routines. Our omniplate software corrects both measurements of optical density to become linear in the number of cells and measurements of fluorescence for autofluorescence. It estimates growth rates and fluorescence per cell as continuous functions of time and enables tens of plate-reader experiments to be analysed together. Data can be exported in text files in a format immediately suitable for public repositories. Plate readers are a convenient way to study cells; omniplate provides an equally convenient yet powerful way to analyse the resulting data.