Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1258961 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Vidua chalybeata (Village indigobird) genome, bVidCha1, merged haplotype
| PRJNA889055 | ENA
Project description:Vidua chalybeata (Village indigobird) genome, bVidCha1, purge dup haplotype
| PRJNA889056 | ENA
Project description:Copy Number Variations (CNVs) were identified performing Comparative Genomic Hybridization (CGH) on 225 patients after whole-genome amplification, using Agilent SurePrint G3 4x180K microarrays. CNVs were further integrated with gene expression (Affymetrix U133+2 arrays) and mutations (targeted DNA resequencing). Complete description of the methods, array quality checks and called segments are available as supplemental material in the corresponding publication.
2019-10-24 | GSE136962 | GEO
Project description:Background: Evolutionary engineering is a powerful approach to isolate suppressor mutants and industrially relevant genotypes. Until recently, DNA microarray analysis was the only affordable genome-wide approach to identify the responsible mutations. This situation has changed due to the rapidly decreasing costs of whole genome (re)sequencing. DNA microarray-based mRNA expression analysis and whole genome resequencing were combined in a study on lactate transport in Saccharomyces cerevisiae. Jen1p is the only S. cerevisiae lactate transporter reported in literature. To identify alternative lactate transporters, a jen1Δ strain was evolved for growth on lactate. Results: Two independent evolution experiments yielded Jen1p-independent growth on lactate (μmax 0.14 and 0.18 h-1 for single-cell lines IMW004 and IMW005, respectively). Whereas mRNA expression analysis did not provide leads, whole-genome resequencing showed different single nucleotide changes (C755G/Leu219Val and C655G/Ala252Gly) in the acetate transporter gene ADY2. Analysis of mRNA levels and depth of coverage of DNA sequencing combined with karyotyping, gene deletions and diagnostic PCR showed that in IMW004 an isochromosome III (~475 kb), which contains two additional copies of ADY2C755G, was formed via crossover between YCLWΔ15 and YCRCΔ6. Introduction of the ADY2 alleles in a jen1 ady2 strain resulted in growth on lactate (μmax 0.14 h-1 for Ady2pLeu219Val and 0.12 h-1 for Ady2pAla252Gly). Conclusions: Whole-genome resequencing of yeast strains obtained from independent evolution experiments enabled rapid identification of a key gene that was not identified by mRNA expression analysis of the same strains. Reverse metabolic engineering showed that mutated alleles of ADY2 (C655G and C755G) encode efficient lactate transporters.
2011-12-21 | GSE31634 | GEO
Project description:Whole-genome resequencing of eight transcription factor mutants and one wild-type, in order to verify the T-DNA insertion site and its uniqueness.
2017-08-15 | GSE102126 | GEO
Project description:Analysis of DNA from 89 oral lesions by whole genome tiling-path array comparative genomic hybridization. Keywords: array comparative genomic hybridization
2009-07-01 | GSE11275 | GEO
Project description:Analysis of DNA from 94 oral lesions by whole genome tiling-path array comparative genomic hybridization. Keywords: array comparative genomic hybridization
2008-12-31 | GSE9193 | GEO
Project description:Leishmaniasis is a neglected tropical disease affecting millions of people worldwide. Emerging drug resistance of Leishmania species poses threaten to the effective control and elimination of this neglected tropical disease. Here we conducted whole genome resequencing, proteome profiling, and comparative analyses of a drug-resistant clinical isolate and two drug-susceptible strains of Leishmania donovani to explore genetic features that might contribute to the establishment of drug resistance in this parasite. By comparative genomic analysis, exclusive variations were identified in the drug-resistant isolate of L. donovani, including 86 copy number variations, 271 frameshift mutations in protein-coding genes and two site mutations in non-coding genes. Comparative proteomic analysis indicated significant differences in protein expression between resistant and susceptible strains of L. donovani, including 69 exclusive detected molecules and 84 consistent down-/up-regulations in the former. Integrating the genomic mutations and proteomic specificities linked nine of the genomic mutations (gene duplication, insertion and deletion) to significantly altered protein expression changes in the drug-resistant clinical isolate. These genetic features were inferred to be associated with nucleotide-binding and fatty acid metabolism (biosynthesis and degradation), which might contribute to fitness-gains allowing for the drug-resistant phenotype of L. donovani. This comparative and integrative work provided deep insights into the molecular basis underlying resistance establishment, suggesting new aspects to be investigated for novel intervention strategies against L. donovani and related species.
2021-09-09 | PXD017089 | Pride