Woodchuck and human liver comparison
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA85019 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Total RNA from adult human and woodchuck liver was analyzed on human membrane arrays. Two human and two woodchuck liver samples were analyzed in duplicate. The samples were numbered H1a, H1b, H2a, H2b, WC1a, WC1b, WC2a, and WC2b. H, represents human liver; WC represents woodchuck liver. The numbers 1 and 2 were the two individual samples. The a and b represent replicates of the same RNA sample. Keywords = liver, adult, normal, human, woodchuck Keywords: other
2003-05-27 | GSE439 | GEO
Project description:Total RNA from adult human and woodchuck liver was analyzed on human membrane arrays. Two human and two woodchuck liver samples were analyzed in duplicate. The samples were numbered H1a, H1b, H2a, H2b, WC1a, WC1b, WC2a, and WC2b. H, represents human liver; WC represents woodchuck liver. The numbers 1 and 2 were the two individual samples. The a and b represent replicates of the same RNA sample. Keywords = liver, adult, normal, human, woodchuck
2010-06-05 | E-GEOD-439 | biostudies-arrayexpress
Project description:The mammalian liver plays important roles in metabolism, detoxification, immune responses, and in severe liver disease in which transplantation is often the only therapeutic option. Model organisms that allow for the longitudinal examination of liver disease progressions are pivotal for the development of new therapeutic modalities. The eastern North American woodchuck is such a model organism that develops chronic hepatitis and liver cancer after infection with woodchuck hepatitis virus, which closely models the human disease. However, the cellular landscape of the woodchuck liver remains unmapped. In this study, we applied single-cell RNA sequencing to profile matched liver and blood from eight healthy woodchucks, performed spatial transcriptomics to examine zonation and annotated these data via a high-quality woodchuck genome reference that we generated. Here, we report woodchuck transcriptomic cell atlases of 63,389 cells from eight healthy woodchuck livers, 26,972 cells from seven healthy woodchuck PBMC samples, and spatial transcriptomics results for two liver slices from one woodchuck, where we observed expected hepatic cellular diversity comparable to human and murine livers. Furthermore, we assessed the inflammatory potential of woodchuck liver resident immune cells through single-nucleus RNA sequencing of PMA/ionomycin-stimulated precision cut liver slices (9,208 nuclei). Our study provides a map of the woodchuck liver, analogous to the human liver map, as a resource for the field to support future studies in this model organism.
2025-04-08 | GSE264112 | GEO
Project description:The mammalian liver plays important roles in metabolism, detoxification, immune responses, and in severe liver disease in which transplantation is often the only therapeutic option. Model organisms that allow for the longitudinal examination of liver disease progressions are pivotal for the development of new therapeutic modalities. The eastern North American woodchuck is such a model organism that develops chronic hepatitis and liver cancer after infection with woodchuck hepatitis virus, which closely models the human disease. However, the cellular landscape of the woodchuck liver remains unmapped. In this study, we applied single-cell RNA sequencing to profile matched liver and blood from eight healthy woodchucks, performed spatial transcriptomics to examine zonation and annotated these data via a high-quality woodchuck genome reference that we generated. Here, we report woodchuck transcriptomic cell atlases of 63,389 cells from eight healthy woodchuck livers, 26,972 cells from seven healthy woodchuck PBMC samples, and spatial transcriptomics results for two liver slices from one woodchuck, where we observed expected hepatic cellular diversity comparable to human and murine livers. Furthermore, we assessed the inflammatory potential of woodchuck liver resident immune cells through single-nucleus RNA sequencing of PMA/ionomycin-stimulated precision cut liver slices (9,208 nuclei). Our study provides a map of the woodchuck liver, analogous to the human liver map, as a resource for the field to support future studies in this model organism.
2025-04-08 | GSE264107 | GEO
Project description:The mammalian liver plays important roles in metabolism, detoxification, immune responses, and in severe liver disease in which transplantation is often the only therapeutic option. Model organisms that allow for the longitudinal examination of liver disease progressions are pivotal for the development of new therapeutic modalities. The eastern North American woodchuck is such a model organism that develops chronic hepatitis and liver cancer after infection with woodchuck hepatitis virus, which closely models the human disease. However, the cellular landscape of the woodchuck liver remains unmapped. In this study, we applied single-cell RNA sequencing to profile matched liver and blood from eight healthy woodchucks, performed spatial transcriptomics to examine zonation and annotated these data via a high-quality woodchuck genome reference that we generated. Here, we report woodchuck transcriptomic cell atlases of 63,389 cells from eight healthy woodchuck livers, 26,972 cells from seven healthy woodchuck PBMC samples, and spatial transcriptomics results for two liver slices from one woodchuck, where we observed expected hepatic cellular diversity comparable to human and murine livers. Furthermore, we assessed the inflammatory potential of woodchuck liver resident immune cells through single-nucleus RNA sequencing of PMA/ionomycin-stimulated precision cut liver slices (9,208 nuclei). Our study provides a map of the woodchuck liver, analogous to the human liver map, as a resource for the field to support future studies in this model organism.
2025-04-08 | GSE264104 | GEO
Project description:The Eastern woodchuck (Marmota monax) is naturally infected with woodchuck hepatitis virus (WHV), a hepadnavirus closely related to the human hepatitis B virus (HBV). The woodchuck is used as an animal model for studying chronic hepatitis B (CHB) and HBV-associated hepatocellular carcinoma (HCC) in humans, but the lack of sequence information has hitherto precluded functional genomics analysis. To address this major limitation of the model, we report here the sequencing, assembly and annotation of the woodchuck transcriptome, together with the generation of custom woodchuck microarrays. Using this new platform, we characterized the transcriptional response to persistent WHV infection and WHV-induced HCC. This revealed that chronic WHV infection, like HBV, is associated with (i) a limited intrahepatic type I interferon response, (ii) intrahepatic induction of markers associated with T cell exhaustion, (iii) elevated levels of suppressor of cytokine signaling 3 (SOCS3) in the liver, and (iv) intrahepatic accumulation of neutrophils. Underscoring the translational value of the woodchuck model, this study also determined that WHV-induced HCC shares molecular characteristics with a subtype of human HCC with poor prognosis. Conclusion: Our data establish the translational value of the woodchuck model and provide new insights into immune pathways which may play a role either in the persistence of HBV infection or the sequelae of CHB. Custom microarrays, generated from sequences obtained in transcriptome sequencing of woodchuck liver and PBMCs, were used to examine liver gene expression in animals chronically infected with WHV (n=13), animals that had resolved WHV infection at least 12 months prior (R; n=11; range 12-18 months), and uninfected animals (U; n=10). Multiple technical replicates per woodchuck sample are included.
2012-04-10 | E-GEOD-36533 | biostudies-arrayexpress
Project description:The Eastern woodchuck (Marmota monax) is naturally infected with woodchuck hepatitis virus (WHV), a hepadnavirus closely related to the human hepatitis B virus (HBV). The woodchuck is used as an animal model for studying chronic hepatitis B (CHB) and HBV-associated hepatocellular carcinoma (HCC) in humans, but the lack of sequence information has hitherto precluded functional genomics analysis. To address this major limitation of the model, we report here the sequencing, assembly and annotation of the woodchuck transcriptome, together with the generation of custom woodchuck microarrays. Using this new platform, we characterized the transcriptional response to persistent WHV infection and WHV-induced HCC. This revealed that chronic WHV infection, like HBV, is associated with (i) a limited intrahepatic type I interferon response, (ii) intrahepatic induction of markers associated with T cell exhaustion, (iii) elevated levels of suppressor of cytokine signaling 3 (SOCS3) in the liver, and (iv) intrahepatic accumulation of neutrophils. Underscoring the translational value of the woodchuck model, this study also determined that WHV-induced HCC shares molecular characteristics with a subtype of human HCC with poor prognosis. Conclusion: Our data establish the translational value of the woodchuck model and provide new insights into immune pathways which may play a role either in the persistence of HBV infection or the sequelae of CHB.
2012-04-11 | GSE36533 | GEO
Project description:We characterized the identity of hepatic macrophages from the uninvolved liver of a WHV-positive (area with no visible tumor) tumor bearing woodchuck that take up NPs using RNA-sequencing (RNA-seq). Data from WHV-infected animal from experiment 3.
2020-04-01 | GSE147273 | GEO
Project description:The Eastern woodchuck (Marmota monax) is naturally infected with woodchuck hepatitis virus (WHV), a hepadnavirus closely related to the human hepatitis B virus (HBV). The woodchuck is used as an animal model for studying chronic hepatitis B (CHB) and HBV-associated hepatocellular carcinoma (HCC) in humans, but the lack of sequence information has hitherto precluded functional genomics analysis. To address this major limitation of the model, we report here the sequencing, assembly and annotation of the woodchuck transcriptome, together with the generation of custom woodchuck microarrays. Using this new platform, we characterized the transcriptional response to persistent WHV infection and WHV-induced HCC. This revealed that chronic WHV infection, like HBV, is associated with (i) a limited intrahepatic type I interferon response, (ii) intrahepatic induction of markers associated with T cell exhaustion, (iii) elevated levels of suppressor of cytokine signaling 3 (SOCS3) in the liver, and (iv) intrahepatic accumulation of neutrophils. Underscoring the translational value of the woodchuck model, this study also determined that WHV-induced HCC shares molecular characteristics with a subtype of human HCC with poor prognosis. Conclusion: Our data establish the translational value of the woodchuck model and provide new insights into immune pathways which may play a role either in the persistence of HBV infection or the sequelae of CHB. Custom microarrays, generated from sequences obtained in transcriptome sequencing of woodchuck liver and PBMCs, were used to examine non-tumor vs. tumor gene expression in liver samples obtained from animals chronically infected with WHV (n=13). Multiple technical replicates per woodchuck sample are included.
2012-04-10 | E-GEOD-36545 | biostudies-arrayexpress
Project description:The Eastern woodchuck (Marmota monax) is naturally infected with woodchuck hepatitis virus (WHV), a hepadnavirus closely related to the human hepatitis B virus (HBV). The woodchuck is used as an animal model for studying chronic hepatitis B (CHB) and HBV-associated hepatocellular carcinoma (HCC) in humans, but the lack of sequence information has hitherto precluded functional genomics analysis. To address this major limitation of the model, we report here the sequencing, assembly and annotation of the woodchuck transcriptome, together with the generation of custom woodchuck microarrays. Using this new platform, we characterized the transcriptional response to persistent WHV infection and WHV-induced HCC. This revealed that chronic WHV infection, like HBV, is associated with (i) a limited intrahepatic type I interferon response, (ii) intrahepatic induction of markers associated with T cell exhaustion, (iii) elevated levels of suppressor of cytokine signaling 3 (SOCS3) in the liver, and (iv) intrahepatic accumulation of neutrophils. Underscoring the translational value of the woodchuck model, this study also determined that WHV-induced HCC shares molecular characteristics with a subtype of human HCC with poor prognosis. Conclusion: Our data establish the translational value of the woodchuck model and provide new insights into immune pathways which may play a role either in the persistence of HBV infection or the sequelae of CHB.
2012-04-11 | GSE36545 | GEO