Microarray data and gene expression statistics for Saccharomyces cerevisiae exposed to simulated asbestos mine drainage

Our plain-English summary of Microarray data and gene expression statistics for Saccharomyces cerevisiae exposed to simulated asbestos mine drainage, by H.E. Driscoll, J.M. Murray, E.L. English, et al (Data in Brief, 2017).

The study

• Authors: H.E. Driscoll, J.M. Murray, E.L. English, T.C. Hunter, K. Pivarski, E.D. Dolci
• Journal: Data in Brief
• Published: 2017;13:37-45
• Read it: PubMed · Publisher · Free full text

Abstract

Here we describe microarray expression data (raw and normalized), experimental metadata, and gene-level data with expression statistics from Saccharomyces cerevisiae exposed to simulated asbestos mine drainage from the Vermont Asbestos Group (VAG) Mine on Belvidere Mountain in northern Vermont, USA. For nearly 100 years (between the late 1890s and 1993), chrysotile asbestos fibers were extracted from serpentinized ultramafic rock at the VAG Mine for use in construction and manufacturing industries. Studies have shown that water courses and streambeds nearby have become contaminated with asbestos mine tailings runoff, including elevated levels of magnesium, nickel, chromium, and arsenic, elevated pH, and chrysotile asbestos-laden mine tailings, due to leaching and gradual erosion of massive piles of mine waste covering approximately 9 km2. We exposed yeast to simulated VAG Mine tailings leachate to help gain insight on how eukaryotic cells exposed to VAG Mine drainage may respond in the mine environment. Affymetrix GeneChip® Yeast Genome 2.0 Arrays were utilized to assess gene expression after 24-h exposure to simulated VAG Mine tailings runoff. The chemistry of mine-tailings leachate, mine-tailings leachate plus yeast extract peptone dextrose media, and control yeast extract peptone dextrose media is also reported. To our knowledge this is the first dataset to assess global gene expression patterns in a eukaryotic model system simulating asbestos mine tailings runoff exposure. Raw and normalized gene expression data are accessible through the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO) Database Series GSE89875 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE89875).

In plain English

This data article describes a laboratory experiment in which the yeast Saccharomyces cerevisiae was grown in water leached from mine tailings collected in 2013 at the Vermont Asbestos Group Mine in northern Vermont, where chrysotile asbestos was mined from the late 1890s to 1993. The authors mixed tailings with deionized water, put the mixture through three freeze-thaw cycles, filtered the water, and used it to make yeast growth media. Four yeast cultures were grown for 24 hours in this simulated mine drainage and three in control media. Gene activity was then measured with microarrays. Based on comparison with earlier stream samples, the authors stated that the lab leachate was a reasonable substitute for real mine drainage. Magnesium was 100 mg/L in the exposed media and 2.6 mg/L in the control media. In the exposed yeast, 735 genes differed from the controls by at least 1.5-fold, at an uncorrected statistical cutoff (404 lower, 331 higher). Of the 761 genes passing a stricter cutoff that corrects for multiple testing, 405 also met that fold-change threshold. The authors noted that the minerals in the tailings were not analyzed for this study.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Laboratory experiment reported as a data article: gene expression (microarray) dataset from yeast exposed to simulated asbestos mine drainage, compared with unexposed controls
• Who was studied: Yeast, Saccharomyces cerevisiae strain NRRL Y-12632 (ATCC 18824): seven cultures in total, four exposed and three controls. Tailings were collected June 19, 2013 from the Lowell Quarry, Vermont Asbestos Group Mine, Lowell, Vermont, USA, and the leachate was prepared in February 2014.
• Exposure: Simulated mine drainage: 250 g of tailings mixed with 250 ml deionized water, put through three freeze-thaw cycles over ten days, then filtered and used to make YPD growth media. Yeast were exposed for 24 hours. The mine produced chrysotile asbestos.
• Main results:
  • The authors reported that the chemistry of the lab-made leachate was similar to surface water from mine-impaired streams, particularly in pH and conductivity, and treated it as a reasonable substitute for VAG Mine drainage.
  • Total magnesium was 100 mg/L in the simulated mine drainage media and 2.6 mg/L in the control media.
  • Principal components analysis separated exposed and control samples into distinct groups, with no significant outliers.
  • 735 genes were differentially expressed between exposed and control yeast. To be counted, a gene had to meet both an unadjusted p less than 0.05 and an absolute fold change of 1.5 or more. Of these, 404 were down-regulated and 331 up-regulated.
  • 761 genes passed the stricter false discovery rate threshold of 0.05; of these, 405 had a fold change greater than 1.5 in either direction.
• The authors' conclusion: The authors stated that, to their knowledge, this is the first dataset to assess global gene expression patterns in a eukaryotic model system simulating exposure to asbestos mine tailings runoff. They made the data publicly available (NCBI GEO Series GSE89875).
• Limitations the authors state:
  • The minerals in the VAG mine tailings were not characterized for this study. The authors relied on earlier studies for their major and minor constituents.

Topics

Medical terms in this study, explained in our Lexicon: Belvidere Mountain, Chrysotile, Ultramafic Rocks, Tailings.

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