Data from: Exploring the habitability of the outer solar system icy moons for the extremotolerant the yeast Rhodotorula frigidalcoholis
Description
Microorganisms adapted to growing at low temperatures are ideal for studying if the icy moons of the solar system could be habitable for Earth life. These moons have been studied with past space missions and have shown to have environmental characteristics which could enable habitability under their subsurface oceans. This dataset summarizes our research using the psychrotolerant yeast Rhodotorula frigidalcoholis exposed to icy moon conditions. The yeast is an optimal candidate for such investigations as it has the ability to grow between 30 and -10°C. Here we present the survival data after the yeast was exposed to the icy moon conditions. These consisted of 7 days of desiccation, 750 Gy of X-ray radiation and 7500 J/m-2 of polychromatic UV radiation combined. The RNA was isolated and sequenced from the yeast prior to, during and after exposure to the icy moon conditions. Sequenced data in this dataset consists of primary (differential expression analysis) and secondary significant known differentiallly expressed genes (DEGs). Data analysis consisted of principal component analysis (PCA) plots generated through the normalization and standardization of the data to the gene expression levels, volcano plots of identified DEGs using the log2fold change on the x-axis and the log10 adjusted p-value on the y-axis. DEGs were separated in cluster of ortholog groups (COGs) using the NCBI database, and gene set enrichment analysis (GSEA) was performed using the DEGs in the FungiFun3 online tool. The data analysis and figure generation was performed using Microsoft Excel and Matplotlib. The data visulization through figure generation was performed by using the Seaborn data visualization library interface for Matplotlib. Our research help us improve our understanding of how such microorganisms could survive on the icy moons in order to understand habitability but also to guide planetary protection.
Files
Steps to reproduce
To reproduce the data analysis python codes are provided as text files and are grouped in a zip file labelled python_codes.zip. The codes in the file include: combined survival.txt used to generate the bar plot displaying the survival of the yeast to icy moon conditions. combined survival and repair.txt used to generate the bar plot displaying the growth of the yeast after exposure to icy moon conditions. PCA plot.txt used to generate the PCA plots. volcano plot. txt used to generate the volcano plots. COG assigner.txt used to assign COG categories from the NCBI database to each gene from the reference genome. COG genome bar.txt used to generate the single bar chart for the genome of the yeast. COG bar chart.txt used to generate the bar charts of DEG shared between comparisons. GSEA bar plot.txt used to generate the bar plots from the GSEA performed with FungiFun3. GSEA clustered heatmap.txt used to generate the clustered heatmaps from the GSEA with FungiFun3. The primary and secondary data are provided as Microsoft Excel files (.xlsx) and are grouped in a zip file labelled primary _and_secondary_data.zip. The data in the files are labelled and include the following: Survival and repair.xlsx containing the survival and growth data of the yeast after exposure to icy moon conditions in terms of relative survival. Control vs Exposed Differential Expression Analysis.xlsx which includes the raw log2fold change and log10 p-adjusted values of each gene identified in the comparison. Control vs Exposed significant Differential Expressed Genes.xlsx which contains the filtered DEGs with an adjusted p-value <0.05 and absolute log2 fold change >1. Control vs Repaired Differential Expression Analysis.xlsx which includes the raw log2fold change and log10 p-adjusted values of each gene identified in the comparison. Control vs Repaired significant Differential Expressed Genes.xlsx which contains the filtered DEGs with an adjusted p-value <0.05 and absolute log2 fold change >1. Exposed vs Repaired Differential Expression Analysis.xlsx which includes the raw log2fold change and log10 p-adjusted values of each gene identified in the comparison. Exposed vs Repaired significant Differential Expressed Genes.xlsx which contains the filtered DEGs with an adjusted p-value <0.05 and absolute log2 fold change >1. COG of genome.xlsx containing the list of COG letters as frequency in the genome. COG of DEGs and shared DEGs.xlsx which includes the frequency of COG values in each comparison as well as the frequency of COG values DEGs shared between comparisons. GSEA.xlsx containing the data used to generate the GSEA pathway bar plots and the GSEA clustered heatmaps for each comparison.
Institutions
- Radboudumc
- Deutsches Zentrum fur Luft und Raumfahrt Institut fur Luft und Raumfahrtmedizin