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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:Restriction site Associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allow RAD tags to serve as genetic markers spread at a high-density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and utilizing an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second novel region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and non-model systems. Keywords: microarray genotyping
2007-01-24 | GSE5773 | GEO
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:Major advances have been made to develop an automated universal 384-well plate sample preparation platform with high reproducibility and adaptability for extraction of proteins from cells within a culture plate. An in-solution digest strategy is employed to generate peptides from the extracted proteins for LC-MS analysis in the 384-well plate. Method evaluation utilized HeLa cells cultured in the 384-well plate ranging from 500 – 10,000 cells. Digestion efficiency was excellent in comparison to the commercial digest peptides standard with minimal sample loss while improving sample preparation throughput by 20 – 40 fold. Analysis of six human cell types, which included two primary cell samples identified and quantified approximately 4,000 proteins for each sample in a single LC-MS/MS injection with as little as 100 – 10,000 cells depending on cell type demonstrating universality of the platform. Implementation of the comprehensive 384-well format protocol for processing cells to clean digested peptides enables large-scale biomarker validation and compound screening through proteomic analysis.
2021-06-14 | PXD019733 | Pride
Project description:Mar1 deletion and RNA enrichment in Cryptococcus neoformans: pilot data for a high-throughput sequencing course. The goal of this project was to generate pilot data in preparation for a summer course on high-throughput sequencing where participants prepared their own RNA-Seq libraries and analyzed the resulting data. This pilot experiment addressed two questions: 1. Does this experimental system (Cryptococcus neoformans H99 wildtype and mar1 deletion mutant grown in YPD and tissue culture media) provide a good dataset for course participants to analyze. 2. Which rRNA depletion method is best to use in the wetlab component of the course. This data was generated in preparation for the intensive summer course on high-throughput sequencing, funded by NIH grant 5R25EB023928-03 "A hands-on, integrative next-generation sequencing course: design, experiment, and analysis".
2021-02-22 | GSE160397 | GEO
Project description:By hybridizing mRNA to oligonucleotide arrays and searching for probes that are outliers in their probe set, we identify and genotype polymorhisms in two strains of yeast (BY, isogenic to S288C, and RM, a wild vineyard strain) and segregants from a cross between the two strains. We then use this mRNA based genotyping approach to study allele-specific expression in diploid hybrids from a cross between BY and RM. A 1:1 mixture of BY and RM parental mRNA is created and hybridized to arrays as a control in these allele-specific expression experiments. The S. cerevisiae strains BY4716, an S288C derivative, and RM11-1a, a haploid Bb32(3) derivative, are described elsewhere (Brem et al. 2002, Yvert et al. 2003). We grew cultures to 10e7 cells/mL in shake flasks at 175 rpm at 300 C in synthetic C medium. We followed the standard Affymetrix protocol for preparation of RNA samples and for hybridization of the samples to Affymetrix YGS98 expression arrays. In total, three cultures of the BY strain, three cultures of the RM strain, one culture of each of the two haploid segregants and the two diploid segregants hybrids, three cultures of the BY-BY hybrid, three cultures of the RM-RM hybrid, and six cultures of the BY-RM hybrid were analyzed. Values calculated using the method described by Zhang et al. (Nat Biotechnol. 21, 818-821). The results are part of Ronald et al. (2005) describing a novel use of oligonucleotide expression arrays to perform genotyping. This method requires the use of individual probe signals, rather than the overall probeset value as is produced by analysis programs such as MAS or RMA.
2004-11-16 | GSE1975 | GEO
Project description:We performed here the transcriptomic profile of 44 segregants from a cross between S288c and 59A (a spore of EC1118 strain). The analysis was performed in wine fermentation condition in stationary phase during nitrogen starvation and in alcoholic stress. These data, associated with an individual genotyping by Affymetrix array allow us to highlight genetic variations involved in perturbation of regulatory network and fermentative behavior.
2013-10-21 | GSE41025 | GEO