Data for: yEvo Lab: viewing mutations in sequencing data
Data files
Mar 11, 2024 version files 1.73 GB
Abstract
Through yEvo Lab, high school students perform evolution experiments to select for yeast mutants that are more resistant to a specific stressor. These mutants will possess a few changes to their genetic code that may contribute to this resistance. We isolated yeast from each experiment and sequenced their genomes to identify their mutations.
This dataset contains the genome sequences of an ancestral yeast strain and a yeast strain evolved in the presence of caffeine, and a list of mutations that a computer program has identified as differences between the ancestor and evolved yeast. These data are used in a tutorial to learn how to use an online genome viewer, the IGV Web App.
README: yEvo Lab: Viewing Mutations In Sequencing Data
https://doi.org/10.5061/dryad.t1g1jwt96
Description of the data and file structure
Through yEvo Lab, high school students perform evolution experiments to select for yeast mutants that are more resistant to a specific stressor. These mutants will possess a few changes to their genetic code that may contribute to this resistance. We isolated yeast from each experiment and sequenced their genomes to identify their mutations.
This dataset contains the genome sequences of an ancestral yeast strain and a yeast strain evolved in the presence of caffeine, and a list of mutations that a computer program has identified as differences between the ancestor and evolved yeast. These data are used in a tutorial to learn how to use an online genome viewer, the IGV Web App (https://igv.org/app/. The tutorial is freely available at https://yevo.org/visualize-sequencing-data.
There is one worksheet file and five (5) data files:
- Worksheet: yEvo_worksheet_ViewingMutationsInSequencingData.pdf
- Ancestor strain sequence files: example_ancestor_YMD4612_comb_R1R2.RG.MD.realign.sort.bam and .bam.bai
- Evolved strain sequence files, from yeast evolved to have high caffeine tolerance: example_evolved_YMD4700_comb_R1R2.RG.MD.realign.sort.bam and .bam.bai
- Mutations listed by computer program in Variant Call Format (VCF) file: example_evolved_YMD4700_called_mutations.txt
The worksheet describes how to use each of the data files.
Sharing/Access information
Please credit yEvo Lab. You can view additional information about this project at https://yevo.org/visualize-sequencing-data
Methods
Yeast (YMD4612) was grown in YPD + 10mM caffeine, and concentration was raised stepwise to 20, 30, and 40mM over seven weeks. A clone (YMD4700) was isolated from the evolved population, and prepared for sequencing as previously described (Taylor et al. G3, DOI: 10.1093/g3journal/jkac246). Briefly, DNA was purified using a phenol-chloroform methodology. This DNA was tagmented using a modified Illumina Tagmentation protocol. Ancestral strain YMD4612 was sequenced to a depth of 165x and evolved clone YMD4700 to depth of 119x.