Microbiome analysis of chronic suppurative otitis media and middle ear cholesteatoma in China
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ABSTRACT:
PROVIDER: PRJNA1082718 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28195620_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR28195621_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR28195622_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR28195623_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR28195624_subreads.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Objective: Otitis media is known to alter expression of cytokine and other genes in the mouse middle ear and inner ear. However, whole mouse genome studies of gene expression in otitis media have not previously been undertaken. Ninety-nine percent of mouse genes are shared in the human, so these studies are relevant to the human condition. Methods: To assess inflammation-driven processes in the mouse ear, gene chip analyses were conducted on mice treated with trans-tympanic heat-killed Hemophilus influenza using untreated mice as controls. Middle and inner ear tissues were separately harvested at 6 hours, RNA extracted, and samples for each treatment processed on the Affymetrix 430 2.0 Gene Chip for expression of its 34,000 genes. Results: Statistical analysis of gene expression compared to control mice showed significant alteration of gene expression in 2,355 genes, 11% of the genes tested and 8% of the mouse genome. Significant middle and inner ear upregulation (fold change >1.5, p<0.05) was seen in 1,081 and 599 genes respectively. Significant middle and inner ear downregulation (fold change <0.67, p<0.05) was seen in 978 and 287 genes respectively. While otitis media is widely believed to be an exclusively middle ear process with little impact on the inner ear, the inner ear changes noted in this study were numerous and discrete from the middle ear responses. This suggests that the inner ear does indeed respond to otitis media and that its response is a distinctive process. Numerous new genes, previously not studied, are found to be affected by inflammation in the ear. Conclusion: Whole genome analysis via gene chip allows simultaneous examination of expression of hundreds of gene families influenced by inflammation in the middle ear. Discovery of new gene families affected by inflammation may lead to new approaches to the study and treatment of otitis media.
2013-07-23 | GSE49128 | GEO
Project description:Objective: Otitis media is known to alter expression of cytokine and other genes in the mouse middle ear and inner ear. However, whole mouse genome studies of gene expression in otitis media have not previously been undertaken. Ninety-nine percent of mouse genes are shared in the human, so these studies are relevant to the human condition. Methods: To assess inflammation-driven processes in the mouse ear, gene chip analyses were conducted on mice treated with trans-tympanic heat-killed Hemophilus influenza using untreated mice as controls. Middle and inner ear tissues were separately harvested at 6 hours, RNA extracted, and samples for each treatment processed on the Affymetrix 430 2.0 Gene Chip for expression of its 34,000 genes. Results: Statistical analysis of gene expression compared to control mice showed significant alteration of gene expression in 2,355 genes, 11% of the genes tested and 8% of the mouse genome. Significant middle and inner ear upregulation (fold change >1.5, p<0.05) was seen in 1,081 and 599 genes respectively. Significant middle and inner ear downregulation (fold change <0.67, p<0.05) was seen in 978 and 287 genes respectively. While otitis media is widely believed to be an exclusively middle ear process with little impact on the inner ear, the inner ear changes noted in this study were numerous and discrete from the middle ear responses. This suggests that the inner ear does indeed respond to otitis media and that its response is a distinctive process. Numerous new genes, previously not studied, are found to be affected by inflammation in the ear. Conclusion: Whole genome analysis via gene chip allows simultaneous examination of expression of hundreds of gene families influenced by inflammation in the middle ear. Discovery of new gene families affected by inflammation may lead to new approaches to the study and treatment of otitis media. There are 8 control samples and 9 samples trans-tympanically injected with H flu 10e9 for 6 hours. Each sample is from a single animal.
2013-07-23 | E-GEOD-49128 | biostudies-arrayexpress
Project description:Objective: Otitis media is known to alter expression of cytokine and other genes in the mouse middle ear and inner ear. However, whole mouse genome studies of gene expression in otitis media have not previously been undertaken. Ninety-nine percent of mouse genes are shared in the human, so these studies are relevant to the human condition. Methods: To assess inflammation-driven processes in the mouse ear, gene chip analyses were conducted on mice treated with trans-tympanic heat-killed Hemophilus influenza using untreated mice as controls. Middle and inner ear tissues were separately harvested at 6 hours, RNA extracted, and samples for each treatment processed on the Affymetrix 430 2.0 Gene Chip for expression of its 34,000 genes. Results: Statistical analysis of gene expression compared to control mice showed significant alteration of gene expression in 2,355 genes, 11% of the genes tested and 8% of the mouse genome. Significant middle and inner ear upregulation (fold change >1.5, p<0.05) was seen in 1,081 and 599 genes respectively. Significant middle and inner ear downregulation (fold change <0.67, p<0.05) was seen in 978 and 287 genes respectively. While otitis media is widely believed to be an exclusively middle ear process with little impact on the inner ear, the inner ear changes noted in this study were numerous and discrete from the middle ear responses. This suggests that the inner ear does indeed respond to otitis media and that its response is a distinctive process. Numerous new genes, previously not studied, are found to be affected by inflammation in the ear. Conclusion: Whole genome analysis via gene chip allows simultaneous examination of expression of hundreds of gene families influenced by inflammation in the middle ear. Discovery of new gene families affected by inflammation may lead to new approaches to the study and treatment of otitis media.
2013-07-23 | GSE49122 | GEO
Project description:Chronic suppurative otitis media (CSOM) and middle ear cholesteatoma (MEC) are two different types of chronic otitis media (COM), and there may be differences in bacterial diversity. Fully exploring the bacterial differences between these two diseases plays an important role in the treatment of the disease and in the study of pathogenic mechanisms. Twelve and twenty-nine patients with CSOM and MEC, respectively, were recruited. Middle-ear lesion tissue was collected intraoperatively after opening the tympanic sinus and mastoid cavity under general anaesthesia and sterile conditions. The full-length 16S rRNA genome sequenced using third-generation sequencing (TGS) was then used to profile the bacterial community of each patient. Principal coordinate analysis (PCoA) showed that PC1 and PC2 could explain more than 50% of the between-group differences. Similarity analysis (ANOSIM) using the Binary Jaccard distance matrix indicated that between-group differences were greater than within-group differences (P < 0.05). Staphylococcus aureus was the most common strain in both groups. At the species level, the abundance of Anaerococcus_octavius was significantly different between both groups (P < 0.05). According to the linear discriminant effect size (LefSe) analysis, at the class and genus levels, Alphaproteobacteria and Bacillus were abundant in the CSOM group, respectively. Peptoniphilus_grossensis and Peptostreptococcaceae_bacterium_oral_taxon_929 were abundant at the species level in the MEC group (P < 0.05). Four COG (Clusters of Orthologous Groups) functions at level 2 were significantly different between the two groups (P < 0.05). The CSOM and MEC groups were inhabited by more diverse microbial communities, and the bacterial diversity of the two diseases differed markedly. This could guide the regular use of antibiotics and decrease the likelihood of multidrug-resistant bacteria formation. Further research on the pathogenic diseases of CSOM and MEC will focus on the functional differences between flora.
2025-02-20 | GSE260673 | GEO
Project description:Objective: Otitis media is known to alter expression of cytokine and other genes in the mouse middle ear and inner ear. However, whole mouse genome studies of gene expression in otitis media have not previously been undertaken. Ninety-nine percent of mouse genes are shared in the human, so these studies are relevant to the human condition. Methods: To assess inflammation-driven processes in the mouse ear, gene chip analyses were conducted on mice treated with trans-tympanic heat-killed Hemophilus influenza using untreated mice as controls. Middle and inner ear tissues were separately harvested at 6 hours, RNA extracted, and samples for each treatment processed on the Affymetrix 430 2.0 Gene Chip for expression of its 34,000 genes. Results: Statistical analysis of gene expression compared to control mice showed significant alteration of gene expression in 2,355 genes, 11% of the genes tested and 8% of the mouse genome. Significant middle and inner ear upregulation (fold change >1.5, p<0.05) was seen in 1,081 and 599 genes respectively. Significant middle and inner ear downregulation (fold change <0.67, p<0.05) was seen in 978 and 287 genes respectively. While otitis media is widely believed to be an exclusively middle ear process with little impact on the inner ear, the inner ear changes noted in this study were numerous and discrete from the middle ear responses. This suggests that the inner ear does indeed respond to otitis media and that its response is a distinctive process. Numerous new genes, previously not studied, are found to be affected by inflammation in the ear. Conclusion: Whole genome analysis via gene chip allows simultaneous examination of expression of hundreds of gene families influenced by inflammation in the middle ear. Discovery of new gene families affected by inflammation may lead to new approaches to the study and treatment of otitis media. There are 6 control samples and 8 samples trans-tympanically injected with H flu 10e9 for 6 hours. Each sample is a pool of 4 animals
2013-07-23 | E-GEOD-49122 | biostudies-arrayexpress
Project description:* Bone signaling in middle ear development * <br/>Common middle ear diseases, such as chronic suppurative otitis media and cholesteatoma, may affect bone behavior in the middle ear air cell system. <br/> This study analyzed gene expression of bone-related signaling factors and gene sets from lining tissues in the developing middle ear of the rat. Candidate gene products were compared with previously published data on middle ear bone metabolism. <br/> Microarray technology was used to identify bone-related genes and gene sets, which were differentially expressed between the adult (quiescent) bulla and young (resorbing/forming) bulla. <br/><br/> * Gene expression of the otic capsule *<br/>The behavior of bone cells within the otic capsule is unique. After occification localized bone remodeling is virtually absent. Human otosclerosis is a localized disease within the otic capsule where the bone starts to remodel pathologically. Disease etiology is unknown and the pathogenesis is only partially elucidated.<br/><br/> The objective of this study is to measure bone-related gene expression of the otic capsule in order to reveal additionally signaling factors responsible for the absent bone remodeling within the otic capsule.<br/><br/> Microarray technology was used to determine genes involved in the bone metabolism, which were differentially expressed between lining tissues from the otic capsule and lining tissues from the middle ear of the rat.
2014-02-20 | E-MTAB-2336 | biostudies-arrayexpress
Project description:Otitis Media Susceptibility and Middle Ear Microbial Shifts due to Gene Variants
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Project description:Otitis Media Susceptibility and Middle Ear Microbial Shifts due to Gene Variants
| PRJNA593081 | ENA
Project description:To investigate the differential expression profiling of circular RNAs (circRNAs) between acquired middle ear cholesteatoma and normal skin, and to identify potential circRNAs contributing to the etiopathogenesis of middle ear cholesteatoma, circRNA microarray analysis and functional prediction were performed.
2021-12-23 | GSE171006 | GEO
Project description:Influenza A virus (IAV) predisposes individuals to secondary infections with the bacterium Streptococcus pneumoniae (the pneumococcus). Infections may manifest as pneumonia, sepsis, meningitis or otitis media (OM). It remains controversial as to whether secondary pneumococcal disease is due to the induction of an aberrant immune response or IAV induced immunosuppression. Moreover, as the majority of studies have been performed in the context of pneumococcal pneumonia, it remains unclear how far these findings can be extrapolated to other pneumococcal disease phenotypes. Here, we demonstrate that the viral hemagglutinin (HA) mediates bacterial OM by inducing a pro-inflammatory response in the middle ear cavity in a replication-dependent manner. Importantly, our findings show that it is the inflammatory response that mediates pneumococcal replication; not viral suppression of the immune system or epithelial damage. This study provide the first evidence that HA induced inflammation drives pneumococcal replication in the middle ear cavity, which has important consequences to the treatment of pneumococcal OM.
2013-01-01 | GSE41098 | GEO