1. Where can I find the inducible transcriptional system library?

The plasmids that contain inducible transcriptional systems driving the expression of yEVenus-PEST can be obtained from Addgene: https://www.addgene.org/browse/article/28215792/

The strains that contain single copies of the reporter constructs can be obtained from National BioResource Project – Yeast database: https://yeast.nig.ac.jp/yeast/by/StrainAllItemsList.jsf?id=29087-29102

The sequences of the used promoters are available on the promoters’ respective webpages.

The raw single-cell data of the transcriptional systems activity are available on the promoter’s respective webpages.

2. How can I compare my promoter’s level of expression to the promoters’ from the library?

You can start by comparing the level of activity of your promoter to the GAL1pr induction in galactose. We introduced an intuitive unit as a measure of promoter’s activity, maxGAL1, which corresponds to average activity of GAL1pr in stationary phase of induction in synthetic complete media containing 3% raffinose and 2% galactose.

3. How can I extract the parameters of induction for my promoter to compare it with the ones from the publication? 

You can use our code: https://github.com/lpbsscientist/promoter-benchmark-model.

4. Where can I find source data from the publication?

Here, or under ‘download single-cell induction data’ on the webpage of the transcriptional system you’re interested in.

5.  How is promoters’ activity measured?

As a reporter of promoters’ activity, we have used a fast-folding bright fluorescent protein optimized for expression in budding yeast, yEVenus. The fluorescence was measured using fluorescent microscopy, by tracking the levels of yEVenus-PEST around and during a 3.5 h induction. The microscopy data was analyzed using YeaZ, a neural-network based tool for segmentation of yeast microscopy images (Dietler, N., Minder, M., Gligorovski, V. et al. A convolutional neural network segments yeast microscopy images with high accuracy. Nat Commun 11, 5723 (2020). https://doi.org/10.1038/s41467-020-19557-4)

5. How are promoters in the library standardized?

To allow direct comparison between the promoters in the library, we designed the budding yeast strains harboring different promoters to be the same in terms of:
– integration locus: all reportes are integrated in the URA3 locus
– copy number: all reportes are integrated in single copies
– the plasmids backbone used as a starting point for cloning
– the sequence between the promoter and the yEVenus reporter

6. I found an error on the website, who can I contact?

For any suggestions or comments about the website, or in case you find any errors, please write to Vojislav Gligorovski.

7.  How to cite us?

If you have used the inducible promoters library characterization for designing your experiments, please cite the following manuscript:
Gligorovski, V., Sadeghi, A. & Rahi, S.J. Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor. Nat Commun 14, 3810 (2023). https://doi.org/10.1038/s41467-023-38959-8