Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional profiling of mouse eosinophils identifies distinct gene signatures following cellular activation

ABSTRACT: Purpose: we aimed to characterized the transcriptional profile of mouse eosinophils in response to stimuli that are associated with Type 1 and Type 2 environments Methods: Eosinophils were purified from the peritoneal cavity of Il5Tg mice and stimulated with IL-4 (i.e. type 2 activated eosinophils), IFN-γ, and a combination of lipopolysaccharide (LPS, i.e. type 1 activated eosinophils) in the presence of IFN-γ. Thereafter, RNA was obtained and the transcriptome signature following each stimulation was determined using RNA sequencing. Raw sequencing reads were trimmed and filtered using fastp, then aligned to mouse genome assembly (GRCm38) using STAR 2.7.2a. Normalization and differential expression analysis were performed in R 4.0.3 using the package DESeq2. Finally, gene ontology annotations were obtained from Ensembl and pathway graphs were obtained from KEGG. Results: RNAseq analysis revealed marked differences, which were driven by the different stimulating conditions Conclusion: We demonstrate that eosinophils are polarized to distinct phenotypes following distinct stimuli. These findings contribute to the growing understanding regarding the heterogeneity of eosinophils and their possible roles in different diseases.

ORGANISM(S): Mus musculus

PROVIDER: GSE189213 | GEO | 2021/12/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Differential regulation of Type 1 and Type 2 mouse eosinophil activation by apoptotic cells

Project description:Purpose: We aimed to characterize the role of apoptotic cells in regulating eosinophils' response to diverse stimuli. Methods:Eosinophils were purified from the peritoneal cavity of Il5Tg mice and stimulated with IL-4 (i.e. type 2 activated eosinophils), IFN-γ, and a combination of lipopolysaccharide (LPS, i.e. type 1 activated eosinophils) and IFN-γ in the presence of apoptotic cells. Thereafter, RNA was obtained and the transcriptome signature following each stimulation was determined using RNA sequencing. Raw sequencing reads were trimmed and filtered using fastp, then aligned to mouse genome assembly (GRCm38) using STAR 2.7.2a. Normalization and differential expression analysis were performed in R 4.0.3 using the package DESeq2. Finally, gene ontology annotations were obtained from Ensembl and pathway graphs were obtained from KEGG. Results:RNAseq analysis revealed that apoptotic cells induce transcriptional changes in eosinophils and resulted in enrichment in pathways related to wounding and cell migration. Conclusion:RNAseq analysis of transcripts that were downregulated by apoptotic cells revealed that apoptotic cells inhibit pathways as defense responses and inflammatory responses and that apoptotic cells augmented eosinophils' response to IL-4.

2022-11-23 | GSE216110 | GEO

Proteomic analysis of human eosinophils stimulated with IFN-gamma and IL-5

Project description:Activated eosinophils is a major cell type to be involved in allergic diseases.IL-5 primarily activates eosinophils and prolongs their survival. However, IFN-gamma is also important as an activator for the cells. The aim of this study is to clarify the role of these cytokines as direct activators for human eosinophils.

2024-06-20 | PXD052615 | JPOST Repository

Interferon gamma down-regulates miR-3473b to promote macrophage activation

Project description:Macrophages are major effector cells and antigen presenting cells of the innate immune system and classical activation of macrophage function requires interferon–γ (IFN-γ) pretreatment (priming) and TLR stimuli, which promotes inflammatory responses though high levels of pro-inflammatory cytokines and lower level of the anti-inflammatory cytokines, resulting in microbicidal and tumoricidal effect. However, the underlying molecular mechanism of IFN-γ priming remains elusive. In this study, we explored the effect of IFN-γ on macrophages at miRNA level and discovered that miR-3473b, which was down-regulated after IFN-γ priming, could attenuate the priming effect of IFN-γ. Molecular study revealed that miR-3473b promoted Akt/GSK3 signaling and IL-10 production through directly targeting PTEN to suppress inflammatory response and tumor-suppressing capability of macrophages. In summary, our data demonstrate that IFN-γ beef up macrophage inflammatory response and tumor suppressing capacity by limiting miR-3473b-mediated PTEN suppression. Our work identified an IFN-γ/miR-3473b/Akt axis in the regulation of macrophage function and activation. the assay was performed with 5 μg total RNA samples from both normal BMM (labeled by Cy3) and BMM primed by IFN-γ (100U/ml) for 4 h(labeled by Cy5), normal BMM serves as control.

2014-10-01 | E-GEOD-50569 | biostudies-arrayexpress

Role for ISGF3II in the Antiviral Activity of IFN-gamma

Project description:Type-I (e.g. IFN-alpha, IFN-beta) and type-II IFNs (IFN-gamma) have antiviral, antiproliferative, and immunomodulatory properties. Both types of IFN signal through the Jak/STAT pathway to elicit antiviral activity, yet IFN-gamma is thought to do so only through STAT1 homodimers while type-I IFNs activate both STAT1- and STAT2-containing complexes such as ISGF3. Here we show that ISGF3II - composed of phosphorylated STAT1, unphosphorylated STAT2, and IRF9 - also plays a role in IFN-gamma-mediated antiviral activity in humans. Using phosphorylated STAT1 as a marker for IFN signaling, western blot analysis of IFN-alpha2a treated human A549 cells revealed that pSTAT1 (Y701) levels peaked at 1h, decreased by 6h, and remained at low levels for up to 48h. Cells treated with IFN-gamma showed a biphasic pSTAT1 response with an early peak at 1-2h and a second peak at 15-24h. Gene expression microarray following IFN-gamma treatment for 24h indicated an induction of antiviral genes that are induced by ISGF3 and associated with a type-1 IFN response. Induction of these genes by autocrine type-I and type-III IFN signaling was ruled out using neutralizing antibodies to these IFNs in biological assays and by qRT-PCR. Despite the absence of autocrine IFNs, IFN-gamma treatment induced formation of ISGF3II. This novel transcription factor complex binds to ISRE promoter sequences, as shown by ChIP analysis of the PKR promoter. STAT2 and IRF9 knockdown in A549 cells reversed IFN-gamma-mediated ISRE induction and antiviral activity - implicating ISGF3II formation as a significant component of the cellular response and biological activity of IFN-gamma. Two treatments using three biological replicates each were performed using three million A549 cells. Each was seeded overnight in 10mL complete RPMI and treated. Three were treated with alpha-IFN and three treated with gamma-IFN for 24h. Control samples were left untreated.

2011-01-19 | E-GEOD-25113 | biostudies-arrayexpress

Role for ISGF3II in the Antiviral Activity of IFN-gamma

2011-01-19 | GSE25113 | GEO

In-depth quantitative proteomics of signal pathways in BV2 microglial cell activation

Project description:Microglia become activated by disturbances in the homeostasis of their local microenvironment. While there are varying degrees of microglia activation, a pro-inflammatory reactive state induced by exposure to stimuli like LPS and IFN-γ. In this study, we identified a total of 5497 proteins in whole cell proteome and 4938 proteins for secretome of activated BV-2 mouse microglia cell line with LPS or IFN-γ using improved shotgun proteomic approach. From the differentially expressed proteins in stimulated microglia, we were able to classify pathways related immune-inflammatory response or metabolism. Moreover, we performed longitudinal quantification of secreted proteins during the detrimental activation of microglia which releases neurotoxic molecules mediated neuronal cell loss in the brain region.

2017-08-09 | PXD006558 | Pride

Single-cell RNA and BCR sequencing of naive B cells cultured in IgG class-switching polarising conditions

Project description:Naive B cells (CD27-IgD+) were obtained from 3 healthy controls and cultured in vitro under anti-IgM, CD40L and IFN-gamma to polarise class-switching towards IgG isotypes. Single-cell RNA and BCR sequencing libraries were prepared at Day 0 (before addition of stimuli), Day 3 and Day 6 of the cell culture time-course. This is intended as a dataset to validate a new computational method sciCSR in enumerating productive and sterile immunoglobulin transcripts as indicators of B cell class switching and maturation dynamics.

2023-07-01 | E-MTAB-13050 | biostudies-arrayexpress

Interferon gamma down-regulates miR-3473b to promote macrophage activation

2014-10-01 | GSE50569 | GEO

Anti-IFN antibody 16 array set

Project description:Timecourse experiment (0hr, 2hr,6hr and 21hr) where RNA was extracted from non-rested PBMCs which were exposed to 4 different conditions- nothing (mock), interferon (IFN)gamma, IFN gamma and a non-specific antibody and IFN gamma with purified patient antibody. The purified patient antibody is demonstrated to have a specific anti-interferon gamma effect over time, with the expression profile in the arrays with IFN gamma plus patient antibody most closely resembling the mock arrays. A disease state experiment design type is where the state of some disease such as infection, pathology, syndrome, etc is studied. Using regression correlation

2005-09-17 | E-GEOD-3319 | biostudies-arrayexpress

IFN-gamma-inducible gene expression in Toxoplasma-infected human fibroblasts

Project description:Human fibroblasts were infected or not with Toxoplasma gondii (Pru strain) for 18 h at a nominal MOI of 3. Cells were subsequently treated with human recombinant interferon gamma (0.5 ng/ml = 30 pM) for 0, 2, 4 and 8 h before RNA was harvested for cDNA microarray experiments. Uninfected samples were named N0, N2, N4 and N8 (i.e., N2 indicated uninfected cells treated with interferon gamma for 2 h); infected samples were named P0, P2, P4 and P8. Duplicate cultures were analyzed for each condition (indicated as "a" and "b"). The reference channel (ch1, green) contained Universal Human Reference RNA. Using a genome-wide microarray analysis we show here a complete dysregulation of interferon-gamma-inducible gene expression in human fibroblasts infected with Toxoplasma. Notably, 46 of the 127 interferon-gamma-responsive genes were induced and 19 were suppressed in infected cells before they were exposed to interferon gamma, indicating that other stimuli produced during infection may also regulate these genes. Following interferon-gamma treatment, none of the 127 interferon-gamma-responsive genes could be significantly induced in infected cells. Groups of assays that are related as part of a time series. Infection: Toxoplasma gondii (18h post-infection) Time: time of IFN-gamma treatment Growth Condition: interferon gamma Keywords: time_series_design

2007-07-19 | GSE8521 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data