Shigella CJ DB project
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REPOSITORIES: ENA
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Project description:Background Compelling evidence indicates that Shigella species, the etiologic agents of bacillary dysentery, as well as enteroinvasive Escherichia coli, are derived from multiple origins of Escherichia coli and form a single pathovar. To further understand the genome diversity and virulence evolution of Shigella, comparative genomic hybridization microarray analysis was employed to compare the gene content of E. coli K-12 with those of 43 Shigella strains from all serotypes. Results For the 43 strains subjected to CGH microarray analyses, the common backbone of the Shigella genome was estimated to contain more than 1,900 open reading frames, with a mean number of 729 undetectable ORFs. The mosaic distribution of absent regions indicated that insertions and/or deletions have led to the highly diversified genomes of pathogenic strains. Conclusion These results support the hypothesis that by gain and loss of functions, Shigella species became successful human pathogens through convergent evolution from diverse genomic backgrounds. Moreover, we also found many specific differences between different lineages, providing a window into understanding bacterial speciation and taxonomic relationships. Keywords: comparative genomic hybridization
2007-07-01 | GSE5212 | GEO
Project description:to analyse the transcriptomic response of human intestinal tissue engrafted in SCID mice to Shigella infection Keywords: infection, Shigella, gene expression, intestinal cell
2008-06-23 | GSE8636 | GEO
Project description:Transcriptional profiling of mouse white adipose tissues. The objective of this study is to explore gene expression profiles of obese adipose tissue by DNA microarray data analysis. Male db/db (BKS.Cg-m+/+ Lepr db/J, 6 weeks old) and db/+ (BKS.Cg-Dock7m +/+ Lepr db/J, 6 weeks old) mice were used in this experiment.
2015-09-01 | E-GEOD-70527 | biostudies-arrayexpress
Project description:This research was detected the differentially expressed circular RNAs in the heart tissues of WT mouse and db/db mouse. We have completed the circRNA Arraystar mouse V.2 analysis of the 3 wt mouse and 3 db/db mouse age 3 month. Whole heart tissue RNA samples were collected and then were digested with RNAse R. Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar?s standard protocols.
2023-03-01 | GSE199133 | GEO
Project description:This program addresses the molecular basis of beta-cell failure associated with the development of type 2 diabetes in the db/db mice. Specifically, which genes are differentially expressed in pancreatic islets of the db/db mice compared to the control db/+ mice?
2013-03-22 | GSE31953 | GEO
Project description:Gene expression of liver tissue from db/db untreated (6x replicates) and db/db treated with 5mg/kg of 3c7.v44 mAb (6x replicates). Anti-GCGR antibody treatment in db/db mice: fig 2b in Solloway et al.
2015-06-02 | GSE68142 | GEO
Project description:Trained immunity is a long-term memory of innate immune cells, generating an improved response upon re-infection. Shigella is an important human pathogen and inflammatory paradigm for which there is no effective vaccine. Using zebrafish larvae we demonstrate that after Shigella priming neutrophils are more efficient at bacterial clearance. We observe that Shigella-induced protection is non-specific and long-lasting, and is unlike training by BCG and β-glucan. Analysis of histone ChIP-seq on primed neutrophils revealed that Shigella training deposits the active H3K4me3 mark on promoter regions of 1612 genes, significantly changing the epigenetic landscape of neutrophils towards enhanced microbial recognition and mitochondrial ROS production. Finally, we demonstrate that mitochondrial ROS plays a key role in enhanced antimicrobial activity of trained neutrophils. It is envisioned that signals and mechanisms we discover here can be used in other vertebrates, including humans, to suggest new therapeutic strategies involving neutrophils to control bacterial infection.
2023-09-13 | GSE217063 | GEO
Project description:diabetes, mouse models, diabetic nephropathy, streptozotocin db/db Keywords: other
2004-01-20 | GSE710 | GEO
Project description:This program addresses the molecular basis of beta-cell failure associated with the development of type 2 diabetes in the db/db mice. Specifically, which genes are differentially expressed in pancreatic islets of the db/db mice compared to the control db/+ mice? The db/db mice islets profiling data was analyzed by identifying genes that were up- and down-regulated at selected p value and fold change in the islets of db/db mice compared to the corresponding db/+ controls.
2013-03-22 | E-GEOD-31953 | biostudies-arrayexpress
Project description:Purpose: RNA seq analysis were to compare and contrast the gene expression profile involved in the dedifferentiation of db/db islets in type 2 diabetes Methods: Islets of wild type, db/+ and db/db were purified using perfusion from 12 week old mice and RNA were isolated. Islated RNA were used in RNA seq to understand the expression pattern Results: Using an optimized data analysis workflow, we mapped about 10 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts WT, db/+ and db/db mice islets with TopHat workflow. Hierarchical clustering of differentially expressed genes uncovered there role in type 2 diabetes. Data analysis with TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: We characterised and identified genes involved in dedifferentiation of islets.
2018-05-08 | GSE107489 | GEO