Inter-species array between human, rat and mouse
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ABSTRACT:
PROVIDER: PRJNA154071 | ENA |
REPOSITORIES: ENA
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Project description:We propose a new microarray method, called an inter-species array, that can measure gene expression levels of multiple species at once. As the array operates simply by changing the probes on an Agilent commercial customized array, and conventional facilities and protocols can be used, the method is cost-efficient. We generated an array for humans, rats and mice that covers 6683 genes. The number of genes is larger than that of previous arrays. We measured the expression of genes in astrocyte cells for humans and rats, and in cortex cells for rats and mice.
2011-11-01 | GSE31201 | GEO
Project description:We propose a new microarray method, called an inter-species array, that can measure gene expression levels of multiple species at once. As the array operates simply by changing the probes on an Agilent commercial customized array, and conventional facilities and protocols can be used, the method is cost-efficient. We generated an array for humans, rats and mice that covers 6683 genes. The number of genes is larger than that of previous arrays. We measured the expression of genes in astrocyte cells for humans and rats, and in cortex cells for rats and mice. Single array with multiple species samples.
2011-11-01 | E-GEOD-31201 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE30978: Gene expression levels with various artificial mutations -- exact match GSE30981: Gene expression levels with various artificial mutations -- with mismatch GSE31201: Inter-species array between human, rat and mouse Refer to individual Series
2011-11-01 | E-GEOD-31202 | biostudies-arrayexpress
Project description:Changes in gene regulation level have long been thought to play an important role in evolution and speciation, especially in primates. Over the past decade, comparative genomic studies have revealed extensive inter-species differences in gene expression levels yet we know much less about the extent to which regulatory mechanisms differ between species. To begin addressing this gap, we performed a comparative epigenetic study in primate lymphoblastoid cell lines (LCLs), to query the contribution of RNA polymerase II (Pol II) and four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) to inter-species variation in gene expression levels. We found that inter-species differences in mark enrichment near transcription start sites are significantly more often associated with inter-species differences in the corresponding gene expression level than expected by chance alone. Interestingly, we also found that first-order interactions among the histone marks and Pol II do not markedly contribute to the degree of association between the marks and inter-species variation in gene expression levels, suggesting that the marginal effects of the five marks dominate this contribution.
2014-11-09 | GSE60269 | GEO
Project description:We analyzed the genome-wide expression profiles of mutant strains of two yeast species in which eight different chromatin regulators and one transcription factor were deleted (one gene deleted in each strain). Comparison of the inter-species expression differences between the wild-types of these species and their mutants showed that deletion of regulators tends to increase the amount of inter-species expression differences, suggestng that the regilators are normally buffering hidden variability. In addition, we measured allele-specific expresion levels of the interspecific hybrid formed by mating each of the two corresponding mutants (deleted for the same regulator). Keywords: Comparative transcriptome analysis
2010-11-01 | GSE23866 | GEO
Project description:We analyzed the genome-wide expression profiles of mutant strains of two yeast species in which eight different chromatin regulators and one transcription factor were deleted (one gene deleted in each strain). Comparison of the inter-species expression differences between the wild-types of these species and their mutants showed that deletion of regulators tends to increase the amount of inter-species expression differences, suggestng that the regilators are normally buffering hidden variability. In addition, we measured allele-specific expresion levels of the interspecific hybrid formed by mating each of the two corresponding mutants (deleted for the same regulator). Keywords: Comparative transcriptome analysis Nine gene deletions were examined. For each gene deletion, there are four datasets - S.cerevisiae and S. paradoxus or the hybrid each with two biological repeats. These four datasets are contained within a single slide of our custom two-species microarray, as it includes two subarrays (blocks) and hybridization was performed with two dyes.
2010-11-01 | E-GEOD-23866 | biostudies-arrayexpress
Project description:Array-based cross-species hybridization between genera of Rhabditidae (Nematoda)
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Project description:Zygosaccharomyces inter-species hybrids as model of hybrid sterility due to transcriptional network incompatibility.
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Project description:Different yeast species in distinct clades within Saccharomycetaceae family are interesting model organisms for inter-species comparative proteomics, in regard to different metabolic properties and genomic architectures. The aim in this analysis is revealing conserved and diverse expression profile of proteome under different culture conditions, including fermentative and non-fermentative growth. Our label-free quantitative proteomics analysis not only uncovered species-specific characters of metabolic proteins expression pattern and also provide intriguing insight into optimized protein cost allocation and evolutionary role for duplicated genes.
2015-11-16 | PXD001865 | Pride