Ontology highlight
ABSTRACT:
PROVIDER: PRJNA826903 | ENA |
REPOSITORIES: ENA
Similar Datasets
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Project description:Small RNA-seq were conducted for iPS cells of human-1 (409-B2/HPS0076), human-2 (Nips-B2/HPS0223), chimpanzee-1 (kiku/0138F-1), and chimpanzee-2 (mari/0274F-2). The human samples were mapped to the human genome (hg38) and the chimpanzee samples were mapped to the chimpanzee genome (panTro5). The mapped reads for individual TE copies (in the repeatmasker tables downloaded from UCSC genome browser) were counted, and those for the same subfamily were summed up. The counts were normalized by RPM (reads per million genome-mapped reads).
2022-10-26 | GSE201297 | GEO
Project description:The chimpanzee is the only model other than man for investigating the pathogenesis of viral hepatitis types A through E. Studies of the host response, including microarray analyses, have relied on the close relationship between these two primate species: chimpanzee samples are commonly tested with human-based reagents. In this study, the host response to two dissimilar viruses, hepatitis E virus (HEV) and hepatitis C virus (HCV), was compared in multiple experimentally-infected chimpanzees. Affymetrix U133+2.0 human microarray chips were used to assess the entire transcriptome in serial liver biopsies obtained over the course of the infections. The comparison utilized a permutational t-test-based analysis of selected time points. More specifically, baseline samples were compared with post-inoculation samples that were strategically chosen based on their relationship to viremia, and probe sequences were aligned to the human and chimpanzee genome sequences to assess their relative sensitivity for detecting differentially expressed genes. Regardless of the viral infection, the alignment of differentially expressed genes to the human genome sequence resulted in a larger number of genes being identified when compared with alignment to the chimpanzee genome sequence. This probably reflects the lesser refinement of gene annotation for chimpanzees. In general, the two viruses demonstrated very distinct temporal changes in host response genes, although both RNA viruses induced genes that were involved in many of the same biological systems, including interferon-induced genes. The host response to HCV infection was more robust than the response to HEV infection.
2010-09-22 | GSE22160 | GEO