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ABSTRACT:
PROVIDER: PRJNA1096426 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Array hybridization data for 611 yeast segregants to determine genotype at each marker. DNA from each segregant was digested with DNAseI, labeled with Cy5-ddATP, and hybridized individually to a custom agilent 8x15k, genotyping array . Note: Tetrad refers to the tetrad from the cross of YJM145 x S288c that each segregant was dissected from. Tag ID refers to unique yeast barcode has been integrated at the ho locus in a segregant.
2012-06-29 | E-MTAB-724 | biostudies-arrayexpress
Project description:In this study, two accessions of Arabidopsis thaliana (Columbia and Landsberg erecta) were crossed and tetrads were obtained using thanks to the the quartet mutation, which keeps the 4 haploid pollen grains from a single meiosis attached together. By fertilising a plant (of ecotype Columbia) with a single tetrad, then selecting seeds from siliques containing exactly four seeds and finally sequencing the 4 developed plants, we can access the complete history of meiotic recombination events occurring in a single male meiosis. Comparison of the genomic sequences (WGS) of the 4 plants in a tetrad makes it possible to identify meiotic COs and NCOS events in each tetrad thanks to the numerous polymorphisms specific to each of the parental genomes. The analysis of the WGS tetrads data consists of genotyping a series of SNV markers (differentiating Columbia and Landsberg) positioned on the five chromosomes for the 4 (M1, M2, M3, M4) individuals of a tetrad, representing the 4 chromatids of each chromosomes. A total of 20 tetrads, the F1 and the two parental accessions Columbia and Landsberg erecta were sequenced.
2024-12-02 | E-MTAB-14435 | biostudies-arrayexpress
Project description:Yeast spores genotyping to analyze the fate of meiotic DNA double strand breaks. For control crossovers are recirpocal events based on the information from two independent spore hybridizations from a unique tetrad were used. Genotyping procedure followed as described in Bourgon et al 2009
2012-01-01 | E-MTAB-508 | biostudies-arrayexpress
Project description:To map post-meiotic segregation (PMS) across the yeast genome, we genotyped the two cells resulting from the first mitotic division of the four spores of 4 tetrads of a YJM789/S96 Saccharomyces cerevisiae hybrid strain. Sporulation was induced, tetrads were dissected, spores let to germinate and the two cells coming from the first mitotic division of each spore were finally dissected. DNA from each of the eight cells in each tetrad was extracted from independent overnight cultures in rich medium and hybridized to microarrays, one array per cell. Each hybridization was used to genotype the corresponding cell and genetic differences between the two cells from the same spore revealed PMS. Therefore there are 32 hybridization files, 2 per spore and 8 per tetrad.
2011-07-13 | E-TABM-1031 | biostudies-arrayexpress
Project description:This Project deals with the sequencing of ITS1 region, which is highly variable both in length and in nucleotide sequence for different yeast using yeast-specific primers ITS1 and ITS2. A total of 19 samples involving different brain regions from patients with different conditions were analysed. Of these, 10 are controls-healthy patients and 9 multiple sclerosis (MS) patients.
| EGAS00001002957 | EGA
Project description:We solved the crystal structure of human ARGONAUTE1 (hAGO1) bound to endogenous 5'-phosphorylated guide RNAs. To identify structural changes that evolutionarily rendered hAGO1 inactive, we compared our structure with published structures of guide-RNA-containing and cleavage-active hAGO2. Aside from mutation of a catalytic tetrad residue, proline residues at positions 670 and 675 in hAGO1 introduce a kink in the cS7 loop and thereby forming a convex surface within the hAGO1 nucleic-acid-binding channel near the inactive catalytic site. We predicted that even upon restoration of the catalytic tetrad, hAGO1-cS7 sterically hinders the placement of a fully-paired guide-target RNA duplex into the endonuclease active site. Consistent with this hypothesis, reconstitution of the catalytic tetrad (R805H) led to low level hAGO1 cleavage activity, whereas combining R805H with cS7 substitutions (P670S and P675Q) substantially augmented hAGO1 activity. Evolutionary changes to hAGO1 were subtle and readily reversible, suggesting that loading of guide RNA and seed-based miRNA-target RNA pairing constrain its sequence drift.
2013-06-20 | GSE48076 | GEO
Project description:The aim of this project was to evaluate the ploidy of a S. cerevisiae *S. kudriavzevii hybrid in comparison to the lab strain S288C. Other wine yeast have been icluded in the project for the global analysis.
2012-02-09 | GSE31703 | GEO
Project description:We used tomato pollen in order to identify pollen stage-specific small non-coding RNAs (sncRNAs) and their target mRNAs. We further deployed elevated temperatures to discern stress responsive sncRNAs. For this purpose high throughput sncRNA-sequencing was performed for three-replicated sncRNAs libraries derived from tomato tetrad, post-meiotic, and mature pollen under control and heat stress conditions.
2015-08-20 | E-MTAB-3830 | biostudies-arrayexpress
Project description:Lipid intermediates derived from sphingolipid metabolism are crucial regulators of mitochondrial function from yeast to humans. Among these intermediates, trans-2-hexadecenal (t-2hex) within the sphingolipid degradation pathway exhibits remarkable efficiency in inducing mitochondria-mediated cell death. In yeast cell cultures, the addition of t-2-hex triggers complete disintegration of the mitochondrial network, leading to subsequent cell death. This effect is particularly pronounced in yeast cells lacking the activity of the t-2-hex degrading enzyme, Hfd1. However, the molecular mechanisms of t-2-hex induction of mitochondrial dysfunction are completely unknown. In this project, we want to exploit the unprecedented power of yeast genetics to unveil novel genetic determinants involved in t-2-hex's pro-apoptotic function. To accomplish this, we employed the SATAY method, which combines saturated transposon mutagenesis with high-throughput sequencing to functionally explore the yeast genome. In our screening approach, hfd1 mutant cells harboring a plasmid-encoded inducible MiniDs transposon were induced by galactose, resulting in extensive integration of the transposon throughout the yeast genome. Cells with the plasmid excised and the transposon genomically integrated were pooled together, creating a high-density transposon library comprising approximately 2.3E+06 independent insertion mutants. Subsequently, the pooled mutant library was subjected to treatment with the mitochondria-mediated death inducer, t-2-hexadecenal. As a control, cells were also incubated with the solvent dimethyl sulfoxide (DMSO), in which hexadecenal is dissolved. Following the treatments, cells were collected for genomic DNA extraction and digestion, using restriction enzymes with frequent four-base pair recognition sites. The resulting library fragments were circularized using T4 DNA ligase, and the transposon-genome junctions were selectively amplified through PCR with outward-facing primers specific to the transposon. Finally, the pooled and purified amplicons were subjected to massive sequencing on an Illumina MiSeq platform. The obtained sequences were then aligned to the reference genome of Saccharomyces cerevisiae, allowing for the mapping of transposon insertions and the calculation of transposon counts per gene. This project enabled the identification of genes required for the resistance and toxicity to t-2hex.
2023-08-31 | E-MTAB-13208 | biostudies-arrayexpress
Project description:we show that a short moderate heat stress during the tetrad stage of pollen development targets vital metabolic pathways ultimately leading to sterility and yield losses in maize.
2019-08-20 | GSE132620 | GEO