IL-36R stimulation of colonic mouse fibroblasts
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ABSTRACT:
PROVIDER: PRJEB10270 | ENA |
REPOSITORIES: ENA
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Project description:Intestinal fibroblasts from the colons of C57BL/6 wild-type mice were grown in the presence or absence of IL-36ÉŁ (30 ng/ml) for 4 hours. The experimental setup included 6 samples from 3 colons in a pairwise design (3 stimulated vs 3 unstimulated). Profiling of whole-genome transcriptomic patterns was performed with 1.2 Âľg high quality total RNA per sample by RNA-seq at the Next Generation Sequencing core unit of the university hospital Erlangen. The sequencing platform was Illumina HiSeq-2500 with high output mode and single-end 100bp fragments. The sequencing library was NuGEN Ovation RNA-Seq Library Prep-Kit. Demultiplexed reads were corrected regarding rRNAs, tRNAs, mt-rRNAs and mt-tRNAs. Alignment against the mus musculus reference genome (Ensemble version 75 for GRCm38) was performed with RNAseq aligner STAR (version 2.4.0.i) and quantification (HTseq count) was done of unique mappings.
2015-12-31 | E-MTAB-3814 | biostudies-arrayexpress
Project description:The objective was to determine the transcriptional effect of IL-17A on primary colonic epithelial cells in various differentiation states in vitro. The three states included 1) stem/progenitor cell spheroids grown in 50% L-WRN media as described in our previous publication (PMID: 24232249), 2) differentiating colonic epithelial spheroids (DM) placed in differentiation media without L-WRN for 24 hours, 3) terminally differentiated colonocyte spheroids placed in differentiation media without L-WRN for 48 hours as described in our previous publication (PMID: 27264604). Each condition was cultured with or without 20ng/ml recombinant mouse IL-17A for the final 24 hours.
2018-04-10 | E-MTAB-6365 | biostudies-arrayexpress
Project description:Previous stimulation experiments of stimulated primary murine colonic fibroblasts with IL-36R ligands for 4h in vitro showed an upregulation of pro-inflammatory cytokines e.g. IL-6, IL-1b and chemokines e.g. CXCL1, CCL2 indicating an important role for IL-36 in inflammation. We were interested in analyzing long-term stimulation (9 days) of intestinal fibroblasts to identify a putative differential expression profile. The experimental setup included 6 samples from 3 colons in a pairwise design (3 stimulated vs 3 unstimulated).
2018-11-19 | E-MTAB-6476 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE40560: Transcriptome analysis in primary fibroblasts from HOIL-1-deficient patients upon TNF-alpha or IL-1beta stimulation GSE40561: Transcriptional analysis of whole blood in patients with auto-inflammatory disorders GSE40838: Transcriptome analysis in peripheral blood mononuclear cells (PBMC) from HOIL-1-deficient patients upon TNF-alpha or IL-1beta stimulation Refer to individual Series
2012-10-28 | E-GEOD-40752 | biostudies-arrayexpress
Project description:IRAK-4 is an essential component of the signal transduction complex downstream of the IL-1- and Toll-like receptors. Though regarded as the first kinase in the signaling cascade, the role of IRAK-4 kinase activity versus its scaffold function is still controversial. In order to investigate the role of IRAK-4 kinase function in vivo, knock-in mice were generated by replacing the wild type IRAK-4 gene with a mutant gene encoding kinase deficient IRAK-4 protein (IRAK-4 KD). Analysis of embryonic fibroblasts and macrophages obtained from IRAK-4 KD mice with a number of experimental techniques demonstrated that they greatly lack responsiveness to stimulation with IL-1b or a Toll-like receptor 7 (TLR7) agonist. One of the techniques used, microarray analysis, identified IRAK-4 kinase-dependent IL-1b response genes in mouse embryonic fibroblasts and revealed that the induction of IL-1b-responsive mRNAs was largely ablated in IRAK-4 KD cells. In summary, our results suggest that IRAK-4 kinase activity plays a critical role in IL-1R/TLR7-mediated induction of inflammatory responses. Experiment Overall Design: The response of mouse embryonic fibroblasts from WT and IRAK4 kinase dead animals to stimulation with IL-1b at two time points was determined. There were 12 samples in total, 6 from WT and 6 from IRAK4 kinase dead cells; for each strain there were 3 conditions: growth for 4 hours without stimulation (the strain-specific control), growth for 1 hour with stimulation, and growth for 4 hours with stimulation; for each condition there were two biological replicates.
2007-11-15 | E-GEOD-6789 | biostudies-arrayexpress
Project description:IRAK-4 is an essential component of the signal transduction complex downstream of the IL-1- and Toll-like receptors. Though regarded as the first kinase in the signaling cascade, the role of IRAK-4 kinase activity versus its scaffold function is still controversial. In order to investigate the role of IRAK-4 kinase function in vivo, ‘knock-in’ mice were generated by replacing the wild type IRAK-4 gene with a mutant gene encoding kinase deficient IRAK-4 protein (IRAK-4 KD). Analysis of embryonic fibroblasts and macrophages obtained from IRAK-4 KD mice with a number of experimental techniques demonstrated that they greatly lack responsiveness to stimulation with IL-1b or a Toll-like receptor 7 (TLR7) agonist. One of the techniques used, microarray analysis, identified IRAK-4 kinase-dependent IL-1b response genes in mouse embryonic fibroblasts and revealed that the induction of IL-1b-responsive mRNAs was largely ablated in IRAK-4 KD cells. In summary, our results suggest that IRAK-4 kinase activity plays a critical role in IL-1R/TLR7-mediated induction of inflammatory responses. Keywords: genetic modification, strain comparison, cell stimulation, time course, inflammatory response
2007-03-30 | GSE6789 | GEO
Project description:Mouse embryonic fibroblasts stimulated with varying doses of FGF2 in conventional hES cell medium were analysed on whole-genome expression chips to reveal altered expression of genes encoding secreted proteins. Keywords: Growth factor stimulation experiment
2006-10-03 | GSE5437 | GEO
Project description:Mouse embryonic fibroblasts stimulated with 40 ng/ml of FGF2 in conventional hES cell medium were analysed on whole-genome expression chips to reveal altered expression of genes encoding secreted proteins. Keywords: Growth factor stimulation experiment
2006-10-03 | GSE5436 | GEO
Project description:Mouse embryonic fibroblasts stimulated with 40 ng/ml of FGF2 in conventional hES cell medium were analysed on whole-genome expression chips to reveal altered expression of genes encoding secreted proteins. Keywords: Growth factor stimulation experiment
2006-10-03 | GSE5435 | GEO