Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Simultaneous genotyping, gene expression measurement, and detection of allele-specific expression

ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE1975 | GEO | 2004/11/16

SECONDARY ACCESSION(S): PRJNA90919

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcription profiling and genotyping, detection of allele specific gene expression of Saccharomyces BY, isogenic to S288C, and RM, a wild vineyard strain

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. (in press) 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.

2008-06-11 | E-GEOD-1975 | biostudies-arrayexpress

eQTL linkages in wine yeasts to decipher regulatory networks in wine fermentation

2013-10-21 | GSE41025 | GEO

Genetic complexity in yeast transcripts

Project description:Haploid segregants from a cross between the yeast strains BY4716 and RM11-1a as in Brem et al. 2002 and Yvert et al. 2003. This series contains all GSE617 samples (re-submitted for convenience), plus 27 additional segregants assayed with the same protocol and the same reference sample as GSE617. Keywords: other

2005-01-20 | GSE1990 | GEO

BYxwild_40

Project description:Expression analysis of F1 haploid segregants from a cross between BY4716 (isogenic to S288c) and a wild isolate collected by R. Mortimer. Each segregant sample was subjected to a dye-swap pair of arrays. All arrays used the same pool of reference BY4716 sample. In sample titles, "BY" alone signifies the reference sample and all other strings represent segregants. All sample titles are of the form S1-S2. S1 indicates the sample whose signal was read as channel 1 (Cy5 labeling, fluorescence at 635 nm) and S2 as channel 2 (Cy3, 532 nm). Keywords: repeat sample

2002-05-01 | GSE37 | GEO

S288c_x_YJM145

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

Bulk Segregant Analysis Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae

Project description:To determine the genomic location of a gene that permits xylose utilization we conducted bulk segregant analysis (BSA) using Affymetrix yeast tiling arrays. BSA works by taking advantage of DNA sequence polymorphisms between different strains and the fact that it is relatively easy to pool large numbers of meiotic spore products (segregants) in yeast. Pooling segregants based on their phenotype allows the region of the genome responsible for the phenotype to be detected. This is because DNA polymorphisms in regions unlinked to the locus causing the phenotype will segregate randomly and be “evened” out, while around the genomic region of interest, sequences or polymorphisms responsible for the trait will be present in all positive segregants, and absent in all negative segregants. In our case, a Simi White wine strain (S. cerevisiae) carrying the locus responsible for xylose utilization was crossed to a laboratory strain of Saccharomyces cerevisiae; this strain was estimated to carry DNA polymorphisms relative to the laboratory strain at a level of approximately .5%. Spores from the Simi White / S288c diploid were screened for the xylose utilization phenotype and 39 positive spores were combined into one pool and 39 negative spores into another pool, and genomic DNA (gDNA) was isolated from each pool. We then hybridized the positive and negative gDNA pools to tiling microarrays that were based on the S288c reference genome with the expectation that regions of the genome derived from Simi White will hybridize less robustly to the array because of the DNA polymorphisms between Simi White and S288c. Log2 ratios of probe intensities were calculated (negative/positive), and a peak appeared in the chromosome XV right subtelomeric region that corresponds to less robust hybridization to the microarray of the positive pool gDNA coming from this region of the genome

2010-04-09 | GSE19120 | GEO

eQTL linkages in wine yeasts to decipher regulatory networks in wine fermentation

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. 56 transcriptomic profiles were performed with Agilent mono-color array. 6 hybridizations were performed for each parental strains: 3 technical replicates for 2 biological replicated samples (59As1 and 59As5; S288Cs1 and S288Cs5). One hybridization was performed for each of the 44 segregants. Using mono-color array, the logarithm base 2 of intensity was directly used after normalization.

2013-10-21 | E-GEOD-41025 | biostudies-arrayexpress

SeaIce, Espegrend, Microscosm, Mnemi

Project description:454 dataset for Hosia, et al. Torstensson et al. Dinasquet et al.

| PRJEB7907 | ENA

Genomic structure of and genome-wide recombination in the Saccharomyces cerevisiae S288C progenitor isolate EM93

Project description:The diploid isolate EM93 is the main ancestor to the widely used Saccharomyces cerevisiae haploid laboratory strain, S288C. In this study, we first hybridise DNA from eight EM93 segregants from two tetrads to Affymetrix genechip S. cerevisiae Tiling 1.0R Arrays to generate a high-resolution overview of the genetic differences between EM93 and S288C. We show that EM93 is heterozygous for many polymorphisms, including large sequence polymorphisms, such as deletions and a Saccharomyces paradoxus introgression. We also find that many of the large sequence polymorphisms are associated with Ty-elements and sub-telomeric regions. We next utilize the hybridization profiles of the 3.2 million Tiling Array probes to identify 2,965 genetic markers, which we then used to design an EM93 genotyping array. By genotyping 120 EM93 tetrads, we deduced the structures of all EM93 chromosomes and found that the average EM93 meiosis produces 144 detectable recombination events, consisting of 87 crossover and 57 non-crossover events; we also identified 203 recombination hot-spots and provide evidence for crossover interference. We find that the effect of heterozygous large sequence polymorphisms on recombination is chromosome position-dependent, with sub-telomeric large sequence polymorphisms having no discernable effect on recombination but non-sub-telomeric large sequence polymorphisms reducing recombination. Finally, we find that recombination hotspots show limited conservation, with some but not all strain-specific hotspots being due to heterozygous non-sub-telomeric large sequence polymorphisms.

2012-06-08 | E-MEXP-3246 | biostudies-arrayexpress

Project description:Finn Et al.

| PRJNA433383 | ENA