Inter-species array between human, rat and mouse
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA154071 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Array-based cross-species hybridization between genera of Rhabditidae (Nematoda)
| PRJNA130825 | ENA
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:Species difference in gene expression effect of trichloroethylene (TCE) between mouse and rat (rat)
| PRJNA107427 | ENA
Project description:Zygosaccharomyces inter-species hybrids as model of hybrid sterility due to transcriptional network incompatibility.
| PRJEB26771 | ENA
Project description:Illumina Infinium HumanMethylation850 BeadChip (also known as Illumina EPIC array, GPL23976) was used to generate DNA methylation data from synthetic DNA from 3 species. The DNA samples from each species were enzymatically manipulated so that they would exhibit 0%, 25%, 50%, 75% and 100% percent methylation at each CpG location, respectively. The variable “ProportionMethylated” (with ordinal values 0, 0.25, 0.5, 0.75, 1) can be interpreted as a benchmark for each CpG that maps to the respective genome. Thus, the DNA methylation levels of each CpG are expected to have a high positive correlation with ProportionMethylated across the arrays measurement for the human species. The human EPIC array was applied to calibration data from mouse (n=15 EPIC arrays, 3 per methylation level) and rat (n=10, 2 per methylation level). The EPIC array data were normalized using the noob method (R function preprocessNoob in minfi).
2021-08-27 | GSE174568 | GEO