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RNAseq of untreated, CSF1-treated, CSF1+QVD-treated, and GM-CSF-treated monocytes

ABSTRACT: RNAseq of untreated, CSF1-treated, CSF1+QVD-treated, and GM-CSF-treated monocytes

PROVIDER: PRJEB20973 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR1989780_1.fastq.gz	Fastqsanger.gz
	ERR1989780_2.fastq.gz	Fastqsanger.gz
	ERR1989790_1.fastq.gz	Fastqsanger.gz
	ERR1989790_2.fastq.gz	Fastqsanger.gz
	ERR1989781_1.fastq.gz	Fastqsanger.gz

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RNAseq of untreated, CSF1-treated, CSF1+QVD-treated, and GM-CSF-treated monocytes

Project description:Caspases, which are key effectors of apoptosis, have demonstrated non-apoptotic functions. One of these functions is the differentiation into macrophages of peripheral blood monocytes exposed to Colony-Stimulating Factor-1 (CSF1). Conversely, GM-CSF induces the differentiation of monocytes into macrophages in a caspase-independent manner. Macrophages generated by CSF1 and GM-CSF have distinct polarity. Macrophage polarization plays an important role in the pathogenesis of diverse human diseases as cancer, leading us to explore if caspase inhibition would affect macrophage polarization. To explore the role of caspases in CSF1 differentiation, we used human monocytes sorted from buffy coats treated by cytokines. We reported that caspase inhibition delays the ex vivo differentiation of peripheral blood monocytes exposed to CSF1 and modifies the phenotype of generated macrophages, e.g. cell shape, surface markers. Moreover, by RNAseq, we observed that the macrophages generated in presence of CSF1 and QVD are different from CSF1-treated monocytes and from GM-CSF-treated monocytes. Cell cycle and focal adhesion-related pathway genes were selectively down-regulated. This study confirms the importance of caspase activation in CSF1 differentiation.

2024-01-01 | E-MTAB-5752 | biostudies-arrayexpress

RNAseq of untreated and CSF1-treated, CSF1+QVD-treated monocytes

Project description:RNAseq of untreated and CSF1-treated, CSF1+QVD-treated monocytes

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Microarray analysis of WT bone marrow myeloid progenitors, BM cultured with GM-CSF and M-CSF, and monocytes treated with GM-CSF

Project description:Analysis of genes induced in DC precursors and in BM cells and monocytes treated with GM-CSF For progenitor arrays, bone marrow progenitors (CMP, GMP, CDP, and pre-cDC) were harvested from WT C57Bl/6 mice. For culture arrays, BM was cultured in the presence of GM-CSF or M-CSF and adherent and non-adherent cells sorted. For monocyte cultures, sorted BM monocytes were treated with GM-CSF for 0, 24 or 48 hours.

2012-05-20 | E-GEOD-37029 | biostudies-arrayexpress

Microarray analysis of WT bone marrow myeloid progenitors, BM cultured with GM-CSF and M-CSF, and monocytes treated with GM-CSF

Project description:Analysis of genes induced in DC precursors and in BM cells and monocytes treated with GM-CSF

2012-05-21 | GSE37029 | GEO

Comparison between CD103+ cDC1s from IL-33-treated Flt3L-BMDCs and GM-CSF-treated Flt3L-BMDCs

Project description:To assess genotypic differences between IL-33-induced CD103+ cDC1s and GM-CSF-induced CD103+ cDC1s IL-33 or GM-CSF was treated at 5 ng/ml on the day 5 of Flt3L-BMDC generation and then the cells were incubated for an additional 5 days Then, we performed RNA sequencing of CD103+ cDC1s isolated from IL-33 or GM-CSF-treated Flt3L-BMDCs

2023-05-30 | GSE226585 | GEO

RNAseq of untreated and CSF1-treated, CSF1+QVD-treated monocytes

Project description:Caspases, which are key effectors of apoptosis, have demonstrated non-apoptotic functions. One of these functions is the differentiation into macrophages of peripheral blood monocytes exposed to Colony-Stimulating Factor-1 (CSF1). Macrophage polarization plays an important role in the pathogenesis of diverse human diseases as cancer, leading us to explore if caspase inhibition would affect macrophage polarization. To explore the role of caspases in CSF1 differentiation, we used human monocytes sorted from buffy coats treated by cytokines. We reported that caspase inhibition delays the ex vivo differentiation of peripheral blood monocytes exposed to CSF1 and modifies the phenotype of generated macrophages, e.g. cell shape, surface markers. Moreover, by RNAseq, we observed that the macrophages generated in presence of CSF1 and QVD are different from CSF1-treated monocytes. This study confirms the importance of caspase activation in CSF1 differentiation.

2024-01-01 | E-MTAB-8088 | biostudies-arrayexpress

mRNA profiling on CART19 cells treated with GM-CSF receptor alpha blockade or GM-CSF blockade

Project description:RNA sequencing was performed on three biological replicates of CART19 alone, GM-CSFRA Ab with CART19, or GM-CSF Ab with CART19

2025-04-04 | GSE200287 | GEO

mRNA profiling on CART19 cells treated with GM-CSF receptor alpha blockade or GM-CSF blockade

Project description:mRNA profiling on CART19 cells treated with GM-CSF receptor alpha blockade or GM-CSF blockade

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miRNA expression microarrays in GM-CSF or GM-CSF+IL6-induced mouse MDSC

Project description:Myeloid-derived suppressor cells (MDSCs) have emerged as major regulators of immune responses in cancer and other pathological conditions. Multiple factors including cytokines, transcription factors and multiple signaling pathways are involved in MDSC differentiation. Cytokines such as granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin(IL-6) etc could in vitro mediate development of MDSCs.IL-6 with GM-CSF mediated MDSC not only had stronger suppressive function but also the dynamics of their suppressive function was different from GM-CSF alone mediated MDSCs.To found a new regulatory factor (s) in tumor and inflammatory environments, we compared GM-CSF and IL-6 mediated MDSCs with GM-CSF alone mediated MDSCs using lncRNA microarray, miRNA microarrays and protein-coding mRNA microarrays.

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Next Generation Sequencing of Beauvericin/LPS/Beauvericin with LPS treated GM-CSF-cultured bone marrow derived cells.

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.

2022-04-08 | GSE192689 | GEO

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