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Single-cell whole-genome sequencing of aneuploid cycling and aneuploid arrested cells

ABSTRACT: Single-cell whole-genome sequencing of aneuploid cycling and aneuploid arrested cells

PROVIDER: PRJEB58407 | ENA |

REPOSITORIES: ENA

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Microarray gene expression study of cycling vs arrested S. Pombe minimal cells

Project description:A minimal cell cycle control module is driving the cell cycle in these S. Pombe cells. During the experiment the cells are arrested or released to cycle through the different phases of the cell cycle. Samples were collected at the indicated times points from arrested and cycling cells and expression of genes were measured by microarrays on an Affymetrix platform.

2016-04-01 | E-GEOD-70438 | biostudies-arrayexpress

Whole genome sequencing of revertants derived from aneuploid Cryptococcus neoformans strains

Project description:In Cyptococcus neoformas, 4 aneuploid strains were spread on YPD plates. We saw colony size variations. We randomly sequenced some large colonies derived from each of the 4 aneuploid strains.

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Whole genome sequencing of revertants derived from aneuploid Cryptococcus neoformans strains

Project description:Whole genome sequencing of revertants derived from aneuploid Cryptococcus neoformans strains

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Whole genome sequencing of spontaneous revertants derived from aneuploid Candida albicans strains

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Whole genome sequencing of spontaneous revertants derived from aneuploid Candida albicans strains

Project description:In Candida albicans, aneuploids are unstable. When grown on YPD-agar plates, aneuploids exhibit colony size variations. In this study, 6 aneuploid strains were spread on YPD-agar plates. The large colonies from each strain were sequenced. The small colonies were sequenced in another project.

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Microarray gene expression study of cycling vs arrested S. Pombe minimal cells

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The environmental stress response causes ribosome loss in aneuploid yeast cells.

Project description:Aneuploidy, a condition characterized by whole chromosome gains and losses, is often associated with significant cellular stress and decreased fitness. However, whether and how cells respond to the aneuploid state has remained controversial. In aneuploid budding yeast, two opposing gene expression patterns have been reported: an environmental stress response (ESR) and a “common aneuploidy gene-expression” (CAGE) signature, in which many ESR genes are oppositely regulated. Here, we investigate and bring clarity to this controversy. We show that the CAGE signature is not an aneuploidy-specific gene expression signature but is the result of euploid control cells, but not aneuploid cells, having grown into stationary phase. Because growth into stationary phase is amongst the strongest inducers of the ESR, the ESR in aneuploid cells was masked when stationary phase euploid cells were used for normalization in transcriptomic studies. When exponentially growing euploid cells are used in gene expression comparisons with aneuploid cells, the CAGE signature is no longer evident in aneuploid cells. Instead, aneuploid cells are found to exhibit the ESR. We further show that the ESR causes a selective loss of ribosomes in aneuploid cells, providing an explanation for the decreased cellular density in aneuploid cells. We conclude that aneuploid budding yeast cells mount the ESR, rather than a CAGE signature, in response to aneuploidy-induced cellular stresses that results in selective ribosome loss.

2020-06-16 | GSE146791 | GEO

No evidence for whole-chromosome dosage compensation or global transcriptomic expression differences in spontaneously-aneuploid mutation accumulation lines of Saccharomyces cerevisiae

Project description:Aneuploidy, the state in which an organism’s genome contains one or more missing or additional chromosomes, often causes widespread genotypic and phenotypic effects. Most often, aneuploidies are deleterious; the most common examples in humans being Down’s syndrome (Trisomy 21) and Turner’s syndrome (monosomy X). However, aneuploidy is surprisingly common in wild yeast populations. In recent years, there has been debate as to whether yeast contain an innate dosage compensation response on the whole-genome level, or if these natural isolates are robust to aneuploidy without such a mechanism. In this study, we tested for differential gene expression in 20 aneuploid and 18 euploid lines of yeast from two previous mutation accumulation experiments, where selection was low and therefore aneuploidies arose spontaneously. We found no evidence for whole-chromosome dosage compensation in aneuploid yeast but did find some evidence for attenuation of expression on a gene-by-gene basis. We additionally found that aneuploidy has no effect on the expression of the rest of the genome (i.e. “trans” genes), and that very few mutually exclusive aneuploid lines shared differentially expressed genes. However, we found a small common differential expression response in the euploid lines, suggesting an effect of mutation accumulation on gene expression. Our findings contribute to our understanding of aneuploidy in yeast and support the hypothesis that there is no innate dosage compensation mechanism at the whole-chromosome level.

2021-03-11 | GSE168674 | GEO

Genome instability of aneuploid Candida glabrata strains

Project description:Genome instability of aneuploid Candida glabrata strains

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Genome instability of aneuploid Candida glabrata strains

Project description:Several aneuploid Candida glabrata strains, each bearing a unique karyotype, were spread on YPD plates. They all exhibited colony size vairations. Randmly 10 large colonies from each strain were sequenced.

2023-06-07 | E-MTAB-12484 | biostudies-arrayexpress

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