E-GEOD-23914
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA130527
PROVIDER: E-GEOD-23914 | ExpressionAtlas | 2015-01-06
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-23914-analysis-methods.tsv | Tabular | |||
| E-GEOD-23914-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-23914-configuration.xml | Xml | |||
| E-GEOD-23914-percentile-ranks.tsv | Tabular | |||
| E-GEOD-23914.condensed-sdrf.tsv | Tabular |
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Similar Datasets
Project description:BACKGROUND: Appendicitis followed by appendectomy (AA) at a young age protects against later inflammatory bowel disease (IBD). Using a novel murine appendicitis model we earlier demonstrated that AA proffered significant protection against subsequent experimental colitis. AIM: To delineate genes and biological pathways involved in the protective effect of AA against subsequent colitis using gene set enrichment analysis (GSEA) of DNA microarray data. METHODS: Appendicitis and appendicectomy was done (5 week old male BALB/c mice) near the most proximal colon (caecal lymphoid follicles) and colonic samples were harvested from the most distal colon. Two consecutive laparotomies were done in control Sham-Sham (SS) mice. RNA was extracted (TRIzol®) from 4 individual colonic samples per group (AA group vs. SS group) with each sample taken independently through Affymetrix® microarray hybridization. For GSEA, data for more than 23,000 genes were exported from Partek and analyzed with GSEA software (with 2852 gene sets encoded) to establish correlates with phenotypes of the gene sets. RESULTS: Distal colonic expression of 636 gene-sets were significantly upregulated in AA group samples (False Discovery Rates (FDR) values < 1 % and p value < 0.001; stringent statistical selection). These were validated by quantitative PCR of 14 selected genes across the immunological spectrum and over time-intervals of 3 days, 14 days and 28 days. CONCLUSIONS: Many key immunological, apoptosis-related and cellular function-associated gene-sets involved in the protective effect of AA in experimental colitis were identified. Further analysis of these profiles and biological pathways will assist utilizing these gene products and manipulating various aspects of these pathways to develop better therapeutic strategies in the management of intractable IBD. Appendicitis and appendicectomy was done (5 week old male BALB/c mice) near the most proximal colon (caecal lymphoid follicles) and colonic samples were harvested from the most distal colon. Two consecutive laparotomies were done in control Sham-Sham (SS) mice. RNA was extracted (TRIzol®) from 4 individual colonic samples per group (AA group vs. SS group) with each sample taken independently through Affymetrix® microarray hybridization. variable_protocol: appendicitis and appendectomy: AA1, AA2, AA3, AA4 variable_protocol: sham/sham surgery: SS1, SS2, SS3, SS4 repeat_biological replicate: AA1, AA2, AA3, AA4 repeat_biological replicate: SS1, SS2, SS3, SS4 Upregulated gene-set linked as supplementary file.
2010-09-01 | E-GEOD-23914 | biostudies-arrayexpress
Project description:BACKGROUND: Appendicitis followed by appendectomy (AA) at a young age protects against later inflammatory bowel disease (IBD). Using a novel murine appendicitis model we earlier demonstrated that AA proffered significant protection against subsequent experimental colitis. AIM: To delineate genes and biological pathways involved in the protective effect of AA against subsequent colitis using gene set enrichment analysis (GSEA) of DNA microarray data. METHODS: Appendicitis and appendicectomy was done (5 week old male BALB/c mice) near the most proximal colon (caecal lymphoid follicles) and colonic samples were harvested from the most distal colon. Two consecutive laparotomies were done in control Sham-Sham (SS) mice. RNA was extracted (TRIzol®) from 4 individual colonic samples per group (AA group vs. SS group) with each sample taken independently through Affymetrix® microarray hybridization. For GSEA, data for more than 23,000 genes were exported from Partek and analyzed with GSEA software (with 2852 gene sets encoded) to establish correlates with phenotypes of the gene sets. RESULTS: Distal colonic expression of 636 gene-sets were significantly upregulated in AA group samples (False Discovery Rates (FDR) values < 1 % and p value < 0.001; stringent statistical selection). These were validated by quantitative PCR of 14 selected genes across the immunological spectrum and over time-intervals of 3 days, 14 days and 28 days. CONCLUSIONS: Many key immunological, apoptosis-related and cellular function-associated gene-sets involved in the protective effect of AA in experimental colitis were identified. Further analysis of these profiles and biological pathways will assist utilizing these gene products and manipulating various aspects of these pathways to develop better therapeutic strategies in the management of intractable IBD.
2010-09-01 | GSE23914 | GEO
Project description:The studies reported here were designed to define in more detail the effector cells responsible for the transfer of protective immunity to young host against P. berghei infection, and to investigate the genes expressed in spleen cells of adult protected rats capable of transferring protection to young rats. Keywords: age, malaria, protection, rat
2006-09-01 | GSE4552 | GEO
Project description:Experimental Design: 1. The goal of the experiment: Age-Related Genome Expression Profiles During Hepatic Ischemia 2. Brief description of the experiment: Hepatic ischemia/reperfusion (I/R) injury is a complication of liver surgery, transplantation and shock and differs with age. In the present study, we sought to determine if the age-dependent response to I/R injury was related to differential gene expression during the ischemic period. Total RNA of young (4-5 weeks) and adult (12-14 months) mice undergoing sham surgery or partial hepatic ischemia for 30, 60, or 90 minutes was analyzed by Affymetrix microarray. Gene expression was filtered based on a change in expression of 1.5-fold relative to respective controls and then analyzed by ANOVA. Significant differences in gene expression were observed between age groups. In young mice, 169 genes were down-regulated, whereas adult mice had 1167 genes down-regulated. Of these, only 28 genes were down-regulated in both young and adult mice. Far fewer genes had increased expression during ischemia. Sixty genes in young mice and 51 genes in adult mice were up-regulated. Of those, none were up-regulated in both young and adult mice. There were no distinct functional patterns of gene regulation in either age group. The data demonstrate significant and widespread changes in hepatic gene expression during the ischemic period that may be important to the age-dependent response to I/R injury. Keywords: treated vs non treated
2008-03-01 | GSE10652 | GEO
Project description:Using these samples, it has been shown that the transcriptional landscape in glomeruli of Ercc1[-/Δ] mice at a rather young age of 14 weeks mimics that of mice which have undergone real-life renal aging. Thus, young Ercc1[-/Δ] mice can be used as a model system for glomerular aging in future studies.
2012-12-21 | GSE43061 | GEO
Project description:Experimental Design: 1. The goal of the experiment: Age-Related Genome Expression Profiles During Hepatic Ischemia 2. Brief description of the experiment: Hepatic ischemia/reperfusion (I/R) injury is a complication of liver surgery, transplantation and shock and differs with age. In the present study, we sought to determine if the age-dependent response to I/R injury was related to differential gene expression during the ischemic period. Total RNA of young (4-5 weeks) and adult (12-14 months) mice undergoing sham surgery or partial hepatic ischemia for 30, 60, or 90 minutes was analyzed by Affymetrix microarray. Gene expression was filtered based on a change in expression of 1.5-fold relative to respective controls and then analyzed by ANOVA. Significant differences in gene expression were observed between age groups. In young mice, 169 genes were down-regulated, whereas adult mice had 1167 genes down-regulated. Of these, only 28 genes were down-regulated in both young and adult mice. Far fewer genes had increased expression during ischemia. Sixty genes in young mice and 51 genes in adult mice were up-regulated. Of those, none were up-regulated in both young and adult mice. There were no distinct functional patterns of gene regulation in either age group. The data demonstrate significant and widespread changes in hepatic gene expression during the ischemic period that may be important to the age-dependent response to I/R injury. Keywords: treated vs non treated 2 age groups of 12 young and 12 adult mice that underwent either 30, 60 or 90 minutes of partial ischemia (n=3) or sham operation (n=3) We used microarray to uncover the genomic response during different time points of ischemia
2010-05-26 | E-GEOD-10652 | biostudies-arrayexpress
Project description:Using these samples, it has been shown that the transcriptional landscape in glomeruli of Ercc1[-/Δ] mice at a rather young age of 14 weeks mimics that of mice which have undergone real-life renal aging. Thus, young Ercc1[-/Δ] mice can be used as a model system for glomerular aging in future studies. The RNAs origin from glomerular tissues of mice of 2 distinct genotypes at 3 distinct stages of age. Between 3 and 6 replicates have been prepared per group.
2012-12-21 | E-GEOD-43061 | biostudies-arrayexpress
Project description:To study the protective effects of preoperative fasting against renal ischemia-reperfusion injury, young-lean as well as aged overweight mice were subjected to three days of fasting or ad libitum food consumption, and gene expressions in kidneys of male mice were analyzed 19 samples (5 young control, 4 young fasted, 5 aged control, 5 aged fasted), each from individual mice
2014-06-03 | E-GEOD-52982 | biostudies-arrayexpress
Project description:The disruption of the mucosal barrier of the digestive tract is a common pathological change in the elderly, which often causes inflammatory bowel disease among old people.Given that microRNA (miRNA) molecules are dysregulated in many diseases, the miRNA expression in young and old normal distal colon mucosa in humans was determined by high-throughput analysis. Three young people (27, 28, and 36 years of age) and 3 aged people (72, 79, and 81 years of age) were enrolled in this study. We used microarray analysis to identify miRNA expression in the distal colon mucosa.
2021-05-26 | GSE174837 | GEO