Project description:To study regulatory differences between species, the field of comparative primate genomics has used several approaches, including the use of post mortem frozen tissues, cell lines, and model organisms. However, there are limited quality cell lines from primates and post-mortem tissues cannot be staged, are not amenable to experimental perturbations and are often subject to high environmental variances. Inducible pluripotent stem cells (iPSCs) are an attractive system to study primate biology in a comparative context. However, the fidelity of iPSC derived cell types to primary tissues needs to be assayed in a comparative primate context before the utility of iPSCs can be fully realized for comparative genomics. In order to comprehensively benchmark the performance of iPSC model systems in a comparative framework, we collected RNA-sequencing from primary adult heart tissue and iPSC derived cardiomyocytes from multiple human and chimpanzee individuals. We identified the optimal parameters of iPSC differentiation into cardiomyocytes that minimized differences between each species and their respective adult tissue counterparts in a balanced manner across species. We found that iPSC derived cardiomyocytes are able to recapitulate 50% of the interspecies gene expression differences identified between human and chimpanzee in primary post mortem heart tissues. Furthermore, we determined that cultured cardiomyocytes appear more similar to adult hearts than any other single tissue in their ability to recapitulate differences in gene regulation between human and chimpanzee.
Project description:Groups of samples used in Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system profiles. Keywords: other
2010-05-03 | GSE2168 | GEO
Project description:Comparative genomics of the waterfowl innate immune system
Project description:Groups of samples used in Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system profiles.
Project description:The Males Experiment: This experiment was done to test the sensitivity of our array in detecting single copy losses of probes to the X chromosome. Males (XO) have just one X chromosome, while hermaphrodites (XX) have two. CB4856 and JU258: This experiment was done to determine the natural copy number variation that exists in a wild C. elegans isolate. Extensive natural copy number variation exists in this strain. gkDf2 (VC100): This control experiment was done to confirm that we could reliably detect a large 50-kb homozygous deletion on chromosome X using this array. gk329 (VC766): This control experiment was done to confirm that we could reliably detect a homozygous 1-kb single-gene deletion on the X chromosome. This deletion targets the gene ceh-39. For gk291 (VC615): This control experiment was done to confirm that we could reliably detect a heterozygous (single copy) single-gene 1-kb deletion on chromsome II. This deletion targets the gene dab-1. All other experiments: This experiment was done in an effort to detect novel balanced single copy losses on chromosome II in mutagenized strains. Mutants were previously screened for homozygous lethal mutations on chromosome II, and these mutations were then balanced with the mIn1 balancer chromosome to generate the mutant strain screened in this experiment. Keywords: comparative genomic hybridization
2006-11-18 | GSE6294 | GEO
Project description:Comparative genomics of genetic diversity and defense system in Shewanella baltica