Chimp 190 biopsy baseline vs post infection
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens Pan troglodytes
PROVIDER: GSE11104 | GEO | 2008/04/10
SECONDARY ACCESSION(S): PRJNA106989
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptional profiling of chimp 190 liver biopsy comparing baseline sample with biopsy taken different days after innoculation with HCV Two-condition experiment, baseline vs. infected at weeks 19, 20, 21 and 32 post infection: One replicate per array.
2008-04-10 | E-GEOD-11104 | biostudies-arrayexpress
Project description:In order to infer the inverse expression relationships between microRNAs and mRNAs during HCV infection, we profiled both microRNA and mRNA expressions in HCV positive (HCV+) and HCV negative (HCV-) human liver biopsy tissue samples. This series includes all mRNA profiles.
2010-03-08 | GSE15331 | GEO
Project description:In order to infer the inverse expression relationships between microRNAs and mRNAs during HCV infection, we profiled both microRNA and mRNA expressions in HCV positive (HCV+) and HCV negative (HCV-) human liver biopsy tissue samples. This series includes all microRNA profiles.
2010-03-08 | GSE15288 | GEO
Project description:Hepatitis A virus (HAV) is a hepatotropic human picornavirus that has been associated only with acute infection. Its pathogenesis is not well understood since there have been few recent studies in animal models using modern methodologies. We characterized HAV infections in three chimpanzees, quantifying viral RNA by qRT-PCR and examining critical aspects of the innate immune response including intrahepatic interferon-stimulated gene expression. We compared these infection profiles with similar studies of chimpanzees infected with hepatitis C virus (HCV), a hepatotropic flavivirus that frequently causes persistent infection. Surprisingly, HAV-infected animals exhibited very limited induction of type I interferon-stimulated genes in the liver compared to chimpanzees with acute resolving HCV infection, despite similar levels of viremia and 100-fold greater quantities of viral RNA in the liver. Minimal ISG15 and IFIT1 responses peaked 1-2 weeks after HAV challenge, then subsided despite continuing high hepatic viral loads. An acute inflammatory response at 3-4 weeks correlated with the appearance of virus-specific antibodies, and both apoptosis and proliferation of hepatocytes. Despite this, HAV RNA persisted in the liver for months, remaining present long after its clearance from serum and feces and revealing dramatic differences in the kinetics of clearance in the three compartments. Viral RNA was detected in the liver for significantly longer (35 to >48 weeks) than HCV RNA in animals with acute resolving HCV infection (10-20 weeks). Collectively, these findings suggest that early HAV infection is far stealthier than HCV infection and represents a distinctly different paradigm in viral-host interactions within the liver. Chimpanzee liver was biopsied during an acute HAV infection. Chimp 1 and 2 had two baseline samples. Chimp 3 used the baselines from chimps 1 and 2. Chimp 1 had 8 samples during the HAV acute infection. Chimp 2 had 9 samples during the HAV acute infection. Chimp 3 had 4 samples during the HAV acute infection.
2011-03-09 | E-GEOD-27850 | biostudies-arrayexpress
Project description:In order to infer the inverse expression relationships between microRNAs and mRNAs during HCV infection, we profiled both microRNA and mRNA expressions in HCV positive (HCV+) and HCV negative (HCV-) human liver biopsy tissue samples. This series includes all microRNA profiles. This series includes microRNA profiles of 36 samples, 24 HCV positives and 12 HCV negatives.
2010-05-06 | E-GEOD-15288 | biostudies-arrayexpress
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. Three chimpanzees were inoculated intravenously with the hepatitis C virus: chimp 1628 was infected with < 100 infectious doses (ID) of the H77 strain (genotype 1a) (30); chimp 1417 was infected with an unknown titer, in serum, of the HC-J6 strain (genotype 2a) (31); chimp 1422 was infected with an unknown titer, in serum, of the T.N. strain (genotype 1a) (35). Four chimpanzees (CH1616, CH1618, CH1374 and CH1375) were inoculated intravenously with 0.5 ml of the HEV SAR55 strain (genotype 1) at approximately 10^6 ID. Grouping of the biological replicates was based on viremia: groups consisted of the first positive week (and the second positive week for HCV), the peak positive week, the last positive week, the first negative week and the fourth negative week. There were 3 biological replicates for HCV. The 4 replicates for HEV were both biological and technical. For chimp 1417, 7 samples were taken between weeks 0 and 17. For chimp 1422, 8 samples were taken between weeks 0 and 13. For chimp 1628, 8 samples were taken between weeks 0 and 19. For chimp 1374, 6 samples were taken between weeks 0 and 8. For chimp 1375, 4 samples were taken between weeks 0 and 8. For chimp 1616, 5 samples were taken between weeks 0 and 7. For chimp 1618, 6 samples were taken between weeks 0 and 8. Normalized probe set level data not provided for individual Sample records. Processed data is available on Series record.
2010-09-21 | E-GEOD-22160 | biostudies-arrayexpress
Project description:To define the skeletal muscle adaptations induced by exercise performed at high altitude hypoxia, we investigated if the gene expression profile of Vastus lateralis muscle was affected by 5000 m-above-sl-expedition. Two-condition experiment, Vastus lateralis muscle biopsy post-expedition vs Vastus lateralis muscle biopsy pre-expedition. Five volunteers/climbers. Biological replicates: 1 pre-expedition sample, 1 post-expedition sample.
2010-11-27 | E-GEOD-25618 | biostudies-arrayexpress
Project description:Muscle biopsy samples were obtained from two groups of male subjects prior to endurance training. The samples were used to predict training responses. Baseline gene expression involving 30 probe sets was able to classify subjects into high and low responders.
2010-02-04 | GSE18583 | GEO
Project description:Muscle biopsy samples were obtained from two groups of male subjects prior to endurance training. The samples were used to predict training responses. Baseline gene expression involving 30 probe sets was able to classify subjects into high and low responders. Resting skeletal muscle sample after an overnight fast.
2010-02-03 | E-GEOD-18583 | biostudies-arrayexpress