Genome-wide SNP Analysis of Furfural Stress

A custom whole-genome SNP array (57 (link)) and a chromosome IV-specific SNP array (23 (link)) were used for LOH analysis of yeast isolates treated with furfural. Genomic DNA extraction from yeast cells and DNA fragmentation (with an average size of about 400 bp) were performed according to a protocol described previously (57 (link)). Genomic DNA from the furfural-treated cells was labeled with Cy5-dUTP, and control DNA (from the cells of fully heterozygous strain JSC24-2 [23 (link)]) was labeled with Cy3-dUTP. Competitive hybridization of the two DNA samples was performed on the SNP microarrays at 62°C, and the ratio of hybridization of the two differentially labeled samples was analyzed as described previously (57 (link)).

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Qi L., Zhu Y.X., Wang Y.K., Tang X.X., Li K.J., He M., Sui Y., Wang P.M., Zheng D.Q, & Zhang K. (2023). Nonlethal Furfural Exposure Causes Genomic Alterations and Adaptability Evolution in Saccharomyces cerevisiae. Microbiology Spectrum, 11(4), e01216-23.

Publication 2023

Bp 400 Cells Cells strain Chromosome Cy3 dutp Cy5 dutp Dna fragmentation Furfural Genomic Heterozygous Hybridization Microarrays Yeast

Corresponding Organization : Zhejiang University

Other organizations : Duke University

Top 5 similar protocols

Variable analysis

independent variables

Treatment with furfural

dependent variables

Loss of heterozygosity (LOH) in yeast isolates

control variables

Genomic DNA extraction and fragmentation protocol
Competitive hybridization on SNP microarrays at 62°C
Cells from fully heterozygous strain JSC24-2 as control DNA

controls

Positive control: Cells from fully heterozygous strain JSC24-2
Negative control: Not explicitly mentioned

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