GM-CSF cultured and LPS stimulated WT and miR-155 KO DC
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE40027 | GEO | 2022/01/01
REPOSITORIES: GEO
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Project description:Purpose: The goals of this study are to compare NGS-derived GM-CSF-cultured bone marrow derived cells transcriptome profiling (RNA-seq) normalized counts and differential expression of genes between different stimulations (untreated, Beauvericin, LPS or Beauvericin with LPS). Methods: mRNA profiles of GM-CSF-cultured bone marrow derived FACS purified MHCII high CD11c+ cells from wild-type C57BL/6N mice that were left untreated or stimulated with Beauvericin, LPS or Beauvericin with LPS for 4h were generated by deep sequencing, in quadruplicate, using the Illumina NextSeq550 system. DNase digested total RNA samples used for transcriptome analyses were quantified (Qubit RNA HS Assay, Thermo Fisher Scientific) and quality measured by capillary electrophoresis using the Fragment Analyzer and the ‘Total RNA Standard Sensitivity Assay’ Results: The reads of all probes were adapter trimmed (Illumina TruSeq). Mapping was done against the Mus musculus (mm39; GRCm39) (June 24, 2020) genome sequence. After grouping of samples (four biological replicates each) according to their respective experimental condition, multi-group comparisons were made and statistically determined using DESeq2. The Resulting P values were corrected for multiple testing by FDR. A P value of <0.05 was considered significant. Conclusions: Our study represents the first detailed analysis of untreated and Beauvericin stimulated GM-CSF-cultured bone marrow derived cells transcriptomes.Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within GM-CSF-cultured bone marrow derived cells. We conclude that Beauvericin activates GM-CSF-cultured bone marrow derived cells inducing inflammatory cytokine,chemokine and Type I IFN production via a TLR4 dependent signaling pathway, but induces a gene expression profile different from LPS.
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2023-05-30 | GSE226585 | GEO
Project description:Purpose: To determine SUMO1 and SUMO2 chromatin profile in a static and dynamic manner in BMDC before and after LPS stimulation, and to determine RNAPolII chromatin occupancy in sumoylation-deficient BMDC compared to wild-type cells. Methods: SUMO1, SUMO2 and RNAPolII chromatin profiles were determined by sequencing BMDC chromatin immunoprecipitated with antibodies specific for SUMO1, SUMO2 and RNAPolII before and after LPS stimulation. Results: We show dynamic occupancy of three distal sites upstream of Ifnb1 gene by SUMO1 and SUMO2, as well as increased RNAPolII recruitment on selected genes. Conclusions: SUMO acts as a regulator of inflammatory and anti-viral gene programs.
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