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RNA-Seq analysis of human neutrophils isolated by different protocols (Polymorphprep and negative selection) and incubated with and without in vitro cytokine stimulation

ABSTRACT: We report gene expression in human neutrophils isolated by two methods: Polymorphprep (~95% purity) and negative selection (~99% purity) from two healthy donors - one donor with low eosinophil contamination of neutrophils and one donor with high eosinophil contamination of neutrophils. We report the effect of the presence of contaminating leukocytes in neutrophil preparations, and in reponse to inflammatory cytokines TNF-alpha and GM-CSF.

ORGANISM(S): Homo sapiens

PROVIDER: GSE70068 | GEO | 2015/09/24

SECONDARY ACCESSION(S): PRJNA287562

REPOSITORIES: GEO

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RNA-Seq analysis of human neutrophils isolated by different protocols (Polymorphprep and negative selection) and incubated with and without in vitro cytokine stimulation

Project description:We report gene expression in human neutrophils isolated by two methods: Polymorphprep (~95% purity) and negative selection (~99% purity) from two healthy donors - one donor with low eosinophil contamination of neutrophils and one donor with high eosinophil contamination of neutrophils. We report the effect of the presence of contaminating leukocytes in neutrophil preparations, and in reponse to inflammatory cytokines TNF-alpha and GM-CSF. Healthy human neutrophils were isolated using Polymorphprep or negative selection, and incubated for 1h in the absence or presence of TNF-alpha or GM-CSF. RNA was analysed by Illumina HiSeq 2000. The results from n=2 donors were analysed as biological replicates for differential expression analysis.

2015-09-24 | E-GEOD-70068 | biostudies-arrayexpress

Expression data from human platelets after purification

Project description:Platelets are small anucleate cells derived from the fragmentation of megakaryocytes and are involved in different biological processes especially hemostasis, thrombosis and immune response. Platelet purification is a crucial step in transcriptomic analysis, and researchers usually encounter the problem of platelet contamination by leukocytes and erythrocytes. Leukocytes contain much more RNA than platelets, thus the presence of few contaminants in platelet preparation can strongly alter transcriptome results. Using microarray technique, we compared transcriptome of platelets from the same donor, purified by common centrifugation method or using magnetic microbeads to eliminate contaminating cells.

2022-03-31 | GSE193664 | GEO

Astrocytic trans-differentiation completes a multicellular paracrine feedback loop required for medulloblastoma tumor growth

Project description:We report the application of RNA-sequencing technology for high-throughput profiling of tumor-associated microglia/macrophage (TAMs). First, we checked the purity of sample by qRT-PCR. We confirmed the high purity of TAMs with rare other cell type contamination. By profiling samples of TAMs purified from five individual medulloblastoma of mouse model, we find that TAMs maintain microglia gene signature even there are decrease of microglia genes and increase of macrophage genes. This study provides the evidence for the application of comprehensive gene profiling towards characterization of cellular origin of cell populations in tumor microenvironment.

2019-12-31 | GSE109750 | GEO

RNAseq analysis of the human neutrophil transcriptome, with and without in vitro cytokine stimulation

Project description:We report cytokine specific changes in gene expression in the human neutrophil transcriptome using TNF-alpha and GM-CSF stimulation of healthy neutrophils Healthy human neutrophils were stimulated with TNF-alpha or GM-CSF for 1h in vitro. RNA was analysed by SOLiD and Illumina sequencing. RNA from one biological donor was sequenced on both platforms, and two different biological donors were sequenced by Illumina.

2013-03-06 | E-GEOD-40548 | biostudies-arrayexpress

Expression profiles of sorted murine lung Eosinophils following allergen challenge

Project description:The eosinophil transcriptome analysis indicated a robust transcription change in eosinophils following allergen challenge in the lung. Eosinophils were FACS-sorted from Saline or OVA challenged lung with high purity and then subjected to genome-wide RNA microarray

2014-05-19 | E-GEOD-57757 | biostudies-arrayexpress

Genome-wide analysis of chromatin landscape in murine bone marrow derived eosinophils

Project description:We applied a global approach using broad-range, next-generation sequecing to identify a repertoire of eosinophil-specific enhancers. H3K4me1, H3K4me3, H3K27ac and PU.1 ChIPseq data was paired with ATAC and gene expression data from bmEos. Transcription factor motif analysis revealed enrichment for PU.1 in eosinophil enhancers, and ChIP-seq confirmed PU.1 binding in enhancer of genes highly expressed in eosinophils. Comparison of identified PU.1-bound enhancers with 3 publically available myeloid datasets (neutrophils, bone marrow derived macrophages and immature granulocytes) revealed 25% of PU.1-bound enhancers were unique to eosinophils - an eosinophil-specific PU.1 regulome. GO analysis of eosinophil-specific PU.1-bound enhancers revealed enrichmend for genes involved in migration, proliferation, degranulation and survival. Collectively, our data identify eosinophil-specific enhancers regulating key eosinophil genes through epigenetic mechanisms and TF binding. These findings are supportive of a dynamic, epigenetic eosinophil regulome underlying eosinophil function and diversity.

2021-06-08 | GSE144951 | GEO

RNAseq of unstimulated human neutrophil granulocytes.

Project description:Human neutrophils were isolated with negative selection (Miltenyi MacsXpress, purity > 99%) from fresh venous blood. RNA was isolated directly after without stimulating the cells.

2019-02-01 | GSE118644 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of lung resident cells cell Transcriptomes

Project description:To examine reaction in lung residential cells to influenza viral infection, lung epithelial cells (AEC), clara cells, DC, Mast cells, macrophages, eosinophil, and neutrophils were isolated from lung of mice infected with influenza viruses at 3 day postinfection.

2021-01-23 | GSE165299 | GEO

Expression data from control, aged and activated neutrophils in mouse blood

Project description:Neutrophils provide immune protection against pathogens but also may promote tissue injury in inflammatory diseases. Although neutrophils are generally considered as a relatively homogeneous population, evidence for heterogeneity is emerging. Under steady-state conditions, neutrophil heterogeneity may arise from ageing and the replenishment by newly released neutrophils from the bone marrow. We used microarray to globally analyze gene expression in aged neutrophils and characterize the inflammatory programs that are activated during the aging process in the circulation. Control, aged and activated neutrophils were sorted directly from mouse blood for RNA extraction and hybridization on Affymetrix microarrays. We transfused whole blood and harvested donor neutrophils marked by the CD45.1 allele 6h later to derive neutrophils that had truly aged in vivo. Sorted neutrophils were compared to control donor neutrophils that had been transferred for only 10 min. Additionally, we harvested circulating neutrophils from TNF-? treated mice for comparison with neutrophils activated by systemic inflammation.

2015-09-24 | E-GEOD-69886 | biostudies-arrayexpress

Metastasis-entrained eosinophils enhance lymphocyte-mediated anti-tumor immunity

Project description:The recognition of the immune system as a key component of the tumor microenvironment (TME) led to promising therapeutics. Since such therapies benefit only subsets of patients, understanding the activities of immune cells in the TME is required. Eosinophils are an integral part of the TME especially in mucosal tumors. Nonetheless, their role in the TME and the environmental cues that direct their activities are largely unknown, especially in metastasis. We report that breast cancer-driven lung metastasis is characterized by resident and recruited eosinophils. Eosinophil recruitment to the metastatic lung was regulated by G protein coupled receptor signaling but independent of CCR3. Functionally, eosinophils promoted lymphocyte-mediated anti tumor immunity. Transcriptome and proteomic analyses identified the TME rather than intrinsic differences between eosinophil subsets as a key instructing factor directing anti tumorigenic eosinophil activities. Specifically, TNF-a/IFN-g-activated eosinophils facilitated CD4+ and CD8+ T cell infiltration and promoted anti-tumor immunity. Collectively, we identify a mechanism by which the TME entrains eosinophils to adopt anti-tumorigenic properties, which may lead to the development of eosinophil-targeted therapeutics.

2021-07-27 | PXD027596 | Pride

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