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Expression profile of IL-1beta stimulated and non-stimulated endothelial cells

ABSTRACT: Complete identification of the bone marrow niche remains one of the most progressing fields. Attempts to identify soluble factors involved in stem cell renewal have been less successful. We have previously shown that endothelial cells (EC) can induce the long-term proliferation of hematopoietic progenitor cells (HPC), especially when they had been subjected to an inflammatory stimulus like interleukins (IL) 1. To identify yet unknown growth factors, we compared the expression profile of IL-1 stimulated and non-stimulated endothelial cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE19240 | GEO | 2010/07/01

SECONDARY ACCESSION(S): PRJNA120771

REPOSITORIES: GEO

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Expression profile of IL-1beta stimulated and non-stimulated endothelial cells

Project description:Complete identification of the bone marrow niche remains one of the most progressing fields. Attempts to identify soluble factors involved in stem cell renewal have been less successful. We have previously shown that endothelial cells (EC) can induce the long-term proliferation of hematopoietic progenitor cells (HPC), especially when they had been subjected to an inflammatory stimulus like interleukins (IL) 1. To identify yet unknown growth factors, we compared the expression profile of IL-1 stimulated and non-stimulated endothelial cells. Human endothelial cells were subjected to IL-1 for 4, 8, and 16 hours. Isolated mRNA was analyzed by oligonucleotide microarray chips covering over 46,000 human genes.

2010-07-30 | E-GEOD-19240 | biostudies-arrayexpress

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RNA-Seq approaches to understand the role of ARNO/Cyth2 on IL-1beta-stimulated synovial fibroblasts.

Project description:The aim of this study was to explore the role of ARNO, also known as Cyth2, in synovial fibroblasts using NGS-derived transcriptome analysis (RNA-seq). Synovial fibroblasts were isolated from mouse synovium, and stimulated with IL-1beta for 12 hours in healthy cells and cells where Cyth2 expression was knocked-down by silencing RNA. Methods: Synovial fibroblasts were extracted from the synovium of healthy mice and expanded in vitro, RNA was extracted from naïve, IL-1β stimulated and IL-1β stimulated ARNO knock-down synovial fibroblast. Methods: Whole Transcriptome Profiling of synovial fibroblasts were generated by deep sequencing, in triplicate, using Illumina NextSeq™ 500 platform. Libraries were prepared using polyA selection (TruSeq stranded mRNA kit). Methods: The sequence reads that passed quality filters were aligned to mouse reference genome (GRCM38) using Hisat2 version 2.1.0. we mapped about 30 million sequence reads per sample (75 bp, paired-end) Methods: Featurecounts version 1.4.6 was used to quantify reads counts. Data quality control, non-expressed gene filtering, median ratio normalization (MRN) implemented in DESeq2 package and identification of differentially expressed (DE) genes were done using the R bioconductor project DEbrowser. Results: Firstly, We detected differentially expressed (DE) genes among three conditions, which pass the threshold of >4 fold, adjp <0.01. Then, we detected DE genes in IL-1β stimulated ARNO knock-down synovial fibroblast compared to IL-1β stimulated synovial fibroblast, which pass the threshold of >2 fold, adjp <0.01. DE genes reflect decreased cellular inflammatory response after ARNO knockdown Conclusions: Our results reflect an ARNO-mediated inflammatory response in synovial fibroblast, provides new opportunitties for targeting fibroblast in chronic arthritis and joint disease.

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Human neutrophils stimulated with IL-4.

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