Datasets for YaliFunTome database
Description
All the data and the metadata are also presented in the form of a searchable database YaliFunTome, to be found via the link: https://sparrow.up.poznan.pl/tsdatabase/ General: The aim of this project was to examine the potential implications of transcription factors (TFs) identified in Yarrowia lipolytica genome in stress resistance and/or in the synthesis of heterologous proteins (recombinant proteins: r-Prots). The amount and potential of the data we gathered from completing experimental design inspired us to present them in the form of a searchable catalog. This database can be used to characterize functional behavior of a specific TF across an array of conditions or to screen for TFs that were responsive to a specific combination of environmental factors in our studies. Experimental setup: In short: A collection of 125 Y. lipolytica strains over-expressing (OE) individually TFs was subjected to extensive phenotype screening under different environmental conditions, and the data processing was assisted by mathematical modeling. It was presumed that apart from genetic engineering of the TFs-encoding genes by their OE, implementation of the environmental perturbations will further manipulate the activation status of the TFs. The search of the TFs within the Y. lipolytica genome and construction of the strains co-over-expressing (co-OE) individually one of 125 identified TFs and a reporter protein (RedStar2) was done previously, by our Colleagues: doi:10.1093/femsyr/foy037. Both genes were cloned under a constitutive promoter pTEF (more details can be found here: doi:10.1093/femsyr/fov052). The TF co-OE strains were cultured under a combination of enviromental conditions. The experimental setup was designed using DoE (Design of Experiments; DesignExpert software; StatSoft) Data presentation Each strain overexpressing an individual TF (TF-OE strain) was tested under an array of conditions, and so was the reference strain. Raw data for: optical density at 600 nm wavelength as a proxy of growth, fluorescence intensity from a reporter protein as a proxy of r-Prot synthesis, are presented in a form of heat-maps of fold change (FC) of a given measure response in the TF-OE strain over the control strain (file RAW DATA YaliFunTome.xlsx). The data were also processed according to the Response Surface Methodology to acquire models describing a behavior of a given read parameter within the range of investigated variables (Model Factor's Contributions.xlsx). The adopted data processing strategy enabled the evaluation of each specific variable's contribution to the response's variability (growth, amount of r-Prot) elicited by a given TF-OE strain. This evaluation is presented in Factor's Contribution tables indicating the dominant level of a variable (color-coded and as +1 or -1, according to the adopted coding system) and a percentage contribution of the variable to the response.
Files
Steps to reproduce
All the relevant informaction are described and illustrated in detail: experimental setup: https://sparrow.up.poznan.pl/tsdatabase/?page=setup Data presentation: https://sparrow.up.poznan.pl/tsdatabase/?page=presentation Control strain: https://sparrow.up.poznan.pl/tsdatabase/?page=reference
Institutions
Categories
Funding
Narodowe Centrum Nauki
2021/41/B/NZ9/00086