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ABSTRACT:
PROVIDER: PRJNA629499 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:microarray experiment to test the gene expression in long term lines of mutator and non-mutator yeast. Here we use an experimental evolution approach to investigate the conditions required for evolution of a reduction in mutation rate and the mechanisms by which populations tolerate the accumulation of deleterious mutations. We find that after ~6700 generations four out of eight experimental mutator lines had evolved a decreased mutation rate.
2012-02-02 | GSE35440 | GEO
Project description:microarray experiment to test the gene expression in long term lines of mutator and non-mutator yeast. Here we use an experimental evolution approach to investigate the conditions required for evolution of a reduction in mutation rate and the mechanisms by which populations tolerate the accumulation of deleterious mutations. We find that after ~6700 generations four out of eight experimental mutator lines had evolved a decreased mutation rate. 2 condition experiment, derived experimental evolution strains compared to their ancestor strain. We compared the expression profile of one of the mutator lines (m8) after 6700 generations with its mutator ancestor, and as a control, an evolved non mutator after 6700 generations was compared to to its non-mutator ancestor. In order to prepare cells for expression microarray, glass tubes containing 3 ml of YPD were inoculated from overnight cultures, and grown until the OD600 was approximately 0.3.
2012-02-02 | E-GEOD-35440 | biostudies-arrayexpress
Project description:We assess the prevalence of polygenic evolution in pathways between the yeasts S. cerevisiae and S. bayanus. We first established short-read sequencing methods to detect cis-regulatory variation in a diploid hybrid between the species. We then formulated an analytic strategy to test for the scenario in which selective pressure in one species, to increase or decrease the activity of a pathway, has driven the accumulation of cis-regulatory variants that act in the same direction on gene expression. Application of this test revealed a variety of yeast pathways with evidence for directional regulatory evolution. Measurement of allele-specific expression of each ortholog in a diploid hybrid between Saccharomyces species
2010-02-22 | E-GEOD-19837 | biostudies-arrayexpress
Project description:Whole genome re-sequencing of mutator yeast
| PRJDB43 | ENA
Project description:Genome expression analysis between the yeast wine strain L-846 (diploid heterozygous) and spore derived from it (diploid homozygous).
2010-06-30 | GSE21214 | GEO
Project description:We assess the prevalence of polygenic evolution in pathways between the yeasts S. cerevisiae and S. bayanus. We first established short-read sequencing methods to detect cis-regulatory variation in a diploid hybrid between the species. We then formulated an analytic strategy to test for the scenario in which selective pressure in one species, to increase or decrease the activity of a pathway, has driven the accumulation of cis-regulatory variants that act in the same direction on gene expression. Application of this test revealed a variety of yeast pathways with evidence for directional regulatory evolution.
2010-02-22 | GSE19837 | GEO
Project description:We report the high-throughput profiling of histone modification (H3K9me2) or histone variant CNEP-A/Cnp1 in fission yeast Schizosaccharomyces pombe. By obtaining 1-10 ng immunoprecipitated DNA, we generated genome-wide H3K9me2 or CENP-A/Cnp1 maps of heterozygous deletion diploid mhf2∆/+ and the meiotic haploid progeny of heterozygous deletion diploid wip1∆/+, mhf1∆/+ and mhf2∆/+ in fission yeast. We find that centromere inactivation and neocentromere formation occur independently and postzygotically in single depletion of CENP-T-W-X-S.
2019-09-28 | GSE117954 | GEO
Project description:An enduring issue in evolutionary and cancer biology is how replication infidelity influences genome composition and vice versa. Here we examine this issue by sequencing the genomes of diploid budding yeast strains that are either mismatch repair (MMR) proficient or deficient and encode wild type or mutator variants of the three major nuclear DNA replicases. Analysis of over 43,000 mutations that accumulated in the absence of selective pressure demonstrates that the nuclear DNA replication machinery generates less than one mismatch per genome and in combination with MMR, achieves a genome-wide per base error rate of 1.7 x 10-10. Absent both MMR and purifying selection, replication error patterns strongly depend on replication origin proximity, replication fork direction, and the local DNA sequence. Preferred sequences were observed for base substitutions and deletions. Error rates also vary with replication time, in linker versus nucleosome-bound DNA, in 5'- and 3'-untranslated regions, in coding regions and in intergenic DNA. This genome-wide view shows that replication fidelity is amazingly high but heterogeneous, in patterns that suggest the underlying mechanisms by which replication modulates genome stability and composition and vice versa. Six to ten isolates were sequenced for each combination of DNA polymerase (WT, pol1-L868M, pol2-M644G, pol3-L612M) and mismatch repair (proficient, deficient) genotypes. A single WT isolate was sequenced following micrococcal nuclease digestion.
2014-08-25 | E-GEOD-56939 | biostudies-arrayexpress
Project description:We created a mutator protein. The mutator, was prepared by fusing a PmCDA1 (Petromyzon marinus Cytidine DeAminase) and E.coli RNA polymerase alpha subunit(EcoRNAP alpha). After 120 cycles, whole genome sequencing was performed on the wild type and evolved sample. After characterization of the mutation capacity of our mutator, we evolved a sucrose utilization strain and we sequenced Suc strain.
2021-05-03 | E-MTAB-10368 | biostudies-arrayexpress