E-GEOD-23630
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA129929
PROVIDER: E-GEOD-23630 | ExpressionAtlas | 2025-01-24
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-23630-analysis-methods.tsv | Tabular | |||
| E-GEOD-23630-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-23630-configuration.xml | Xml | |||
| E-GEOD-23630-percentile-ranks.tsv | Tabular | |||
| E-GEOD-23630.condensed-sdrf.tsv | Tabular |
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Project description:Background: In the last decade, much attention has been drawn to probiotic bacteria in the context of inflammatory bowel disease (IBD), since the potential of certain strains to attenuate inflammation was demonstrated in several animal experiments and clinical studies. Data in humans elucidating the molecular mechanism of probiotic action are still scarce. To this end, we used an organ culture system of human colon mucosa and investigated the gene expression profiles after treatment with different probiotic bacteria in phorbol 12-myristate 13-acetate (PMA)/ionomycin (IO)) stimulated samples using whole genome microarrays. Moreover, we analyzed changes occurring in the intestinal explants cultured for 8 hours when compared to fresh, directly frozen mucosa, in order to infer the suitability of the system to study an inflammatory stimulus and likely antiinflammatory responses. Results: Culturing intestinal colon fragments during 8 hours elicited differential gene expression in 283 genes, 229 upregulated and 54 downregulated. Upregulated genes were predominantly related to apoptosis, whereas downregulated genes encoded mitochondrial proteins. No specific enrichment of genes related to inflammation or immune response could be detected, confirming the suitability of the system to further study the inmunomodulatory/anti-inflammatory properties of Lactobacillus casei BL23 (BL23), L.plantarum 299v (LP299v) and L.plantarum 299v (A-) (LP299v (A-)), a mutant strain with reduced adhesive properties to enterocytes. Intestinal explants were stimulated with PMA/IO for 3 hours and subsequently incubated with probiotic bacteria for 4 h. ANOVA analysis (p ? 0,01) revealed 205 differentially expressed genes between Control, PMA/IO (Inflamed), and the 3 bacterial treatments. Most importantly, a number of PMA/IO induced genes related to immune response and immune system process such as IL-2, IFN-?, IL17A and pro-inflammatory cytokines CXCL9 and CXCL11 were downregulated by BL23, LP299v and LP299v (A-). The behaviour of the three Lactobacillus strains was quite similar, although their presence induced differential expression of a small number of genes in a strain dependent manner. Conclusion: The human colon organ culture was found to be a suitable model for the study of inflammatory/anti-inflammatory stimuli, and therefore it constitutes a valuable tool to determine the inmunomodulatory effect of probiotic bacteria. The global transcriptional profile evoked by strains BL23, LP299v and LP299v (A-) in artificially inflamed tissue indicated a clear homeostasis restoring effect, including a decrease of the signals produced by activated T cells. Macroscopically healthy colonic intestinal tissue was obtained at surgery from 3 patients. Intestinal explants were treated with PMA and ionomycin for 3 h to induce pro-inflammatory conditions. Then, culture medium was changed and replaced with either medium or medium containing either Lactobacillus casei BL23, Lactobacillus plantarum 299v, or a nonadherent mutant of L. plantarum 299v (A-) and incubated for further 4 hours. In parallel, control intestinal explants were cultured without any treatment of PMA/ionomycin or probiotic bacteria and compared to directly frozen tissue in order to evaluate changes in gene expression which are due solely to the culture conditions.
2012-06-19 | E-GEOD-23630 | biostudies-arrayexpress
Project description:Background: In the last decade, much attention has been drawn to probiotic bacteria in the context of inflammatory bowel disease (IBD), since the potential of certain strains to attenuate inflammation was demonstrated in several animal experiments and clinical studies. Data in humans elucidating the molecular mechanism of probiotic action are still scarce. To this end, we used an organ culture system of human colon mucosa and investigated the gene expression profiles after treatment with different probiotic bacteria in phorbol 12-myristate 13-acetate (PMA)/ionomycin (IO)) stimulated samples using whole genome microarrays. Moreover, we analyzed changes occurring in the intestinal explants cultured for 8 hours when compared to fresh, directly frozen mucosa, in order to infer the suitability of the system to study an inflammatory stimulus and likely antiinflammatory responses. Results: Culturing intestinal colon fragments during 8 hours elicited differential gene expression in 283 genes, 229 upregulated and 54 downregulated. Upregulated genes were predominantly related to apoptosis, whereas downregulated genes encoded mitochondrial proteins. No specific enrichment of genes related to inflammation or immune response could be detected, confirming the suitability of the system to further study the inmunomodulatory/anti-inflammatory properties of Lactobacillus casei BL23 (BL23), L.plantarum 299v (LP299v) and L.plantarum 299v (A-) (LP299v (A-)), a mutant strain with reduced adhesive properties to enterocytes. Intestinal explants were stimulated with PMA/IO for 3 hours and subsequently incubated with probiotic bacteria for 4 h. ANOVA analysis (p ≤ 0,01) revealed 205 differentially expressed genes between Control, PMA/IO (Inflamed), and the 3 bacterial treatments. Most importantly, a number of PMA/IO induced genes related to immune response and immune system process such as IL-2, IFN-γ, IL17A and pro-inflammatory cytokines CXCL9 and CXCL11 were downregulated by BL23, LP299v and LP299v (A-). The behaviour of the three Lactobacillus strains was quite similar, although their presence induced differential expression of a small number of genes in a strain dependent manner. Conclusion: The human colon organ culture was found to be a suitable model for the study of inflammatory/anti-inflammatory stimuli, and therefore it constitutes a valuable tool to determine the inmunomodulatory effect of probiotic bacteria. The global transcriptional profile evoked by strains BL23, LP299v and LP299v (A-) in artificially inflamed tissue indicated a clear homeostasis restoring effect, including a decrease of the signals produced by activated T cells.
2012-06-20 | GSE23630 | GEO
Project description:The data is supplementary to the RNA-seq analysis of LPS and palmitate stimulation of THP-1 macrophages (E-MTAB-6064), where palmitate for the cell treatment was dissolved in sodium hydroxide and coupled with BSA at a molar ratio 7.5:1. Here we stimulated THP-1 macrophages with the corresponding concentration of BSA (4%) and NaOH (0.4 mM) in the presence of 10 nM phorbol 12-myristate 13-acetate (PMA) for 24 hours added to the standard RPMI 1640 medium with 10% fetal bovine serum (FBS) to estimate the effects and compared them with unstimulated THP-1 macrophages cultured in RPMI 1640 medium with 10% FBS and 10nM PMA.
2019-05-17 | E-MTAB-6439 | biostudies-arrayexpress
Project description:Gene expression profiling was analyzed using A549 cells that were treated with glucose deprivation (GD) or GD + phorbol-12-myristate-13-acetate (PMA).
2013-09-16 | GSE24271 | GEO
Project description:Gene expression profiling has demonstrated clinical utility as a predictive tool in clinical oncology. We have identified genes associated with invasion of pancreatic cancer, and with potential for identifying early recurrence. We used Affymetrix Human U133 Plus 2.0 microarrays to identify specific predictive profiles in pancreatic cancer, and the evolution of gene expression. We identified distinct classes of up-regulated genes during this process. Primary and metastatic pancreatic cancer cell lines (BxPC-3 and AsPC-1), were stimulated with with phorbol-12-myristate 13-acetate (PMA), a known inducer of invasion. Affymetrix gene expression microarray analysis was performed, comparing PMA stimulated BxPC-3 and AsPC-1 gene expression to unstimulated controls, and also PMA stimulated BxPC-3 verses stimulated AsPC-1 cell lines. Differential gene expression was identified using ArrayAssist bioinformatics software. Gene expression changes were confirmed using quantitative reverse transcription polymerase chain reaction (qRT-PCR) (Assays-on-demand, Taqman, ABI systems). Pathway Assist and GOstat were used to identify pathway and gene ontology changes.
2011-01-01 | E-GEOD-22973 | biostudies-arrayexpress
Project description:Purpose: Treatment of midgestation chorionic villus explants with recombinant IFN-b leads to morphological changes including formation of syncitial knots. However, treatment of explants with IFN-l, which is constitutively expressed by syncytiotrophoblasts, is not sufficient to cause these same changes. To understand the different transcriptional changes induced by IFN-b and IFN-l and underlying cause of these morphological changes, we performed RNAsequencing after these different treatments. Methods: Chorionic villi of 18-21 gestation week placentas were dissected. Explants were cultured in DMEM F/12 with 1000 U recombinant IFN-b or 1000U recombinant IFN-l for 24 hours. RNA was then isolated from explants, and RNAsequencing was performed to assess transcriptional changes. Results/ Conclusions: IFN-b but not IFN-l induces interferon stimulated genes (ISGs) in mid gestation chorionic villus explants.
2017-12-31 | GSE104348 | GEO
Project description:We sequenced mRNA from cultured HeLa cells transfected with control or HNRNPU siRNA to compare gene expression level in PMA/Ca2+ ionophore stimulated condition
2020-03-31 | GSE138668 | GEO
Project description:To determine the effects of Th1-cytokines (IL-12 + IFN-gamma) or retinoic acid (RA) on expanding human Tregs isolated from pediatric thymus. Cells were stimulated after isolation and cultured for 13 days before RNAsequencing was performed.
2018-05-24 | GSE112923 | GEO
Project description:THP-1 cells were treated with phorbol 12-myristate 13-acetate (PMA) at 25μg/ml for 48h.Then remove PMA and rest for 24h to obtain M0 macropahges. Further applied LPS and IFNγ or IL-4 and IL-13 for 24h to obtain M1, M2 macrophages, respectively. During polarization, cells were treated with prostaglandin E2 or MEHP.Then M1,M2 cells were collected and applied to RNA-sequencing. We found that PGE2 and MEHP significantly impacted metabolic signature of macrophages.
2021-06-28 | GSE159120 | GEO
Project description:Whole transcriptome amplification of RNA purified from colon explants cultured with different forms of HIV (free, complement opsonized and complement and antibody opsonized HIV) or mock treated for 24h.
2020-09-23 | GSE149749 | GEO