Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling by RNA sequencing of MelanA- and caIKK-treated monocyte-derived dendritic cells

ABSTRACT: We performed RNA-seq experiments on 14 samples to identify differential expressed genes between MelanA- and caIKK-treated monocyte-derived dendritic cells (DCs). DCs electroporated with RNA encoding melanoma antigen recognized by T cells 1 (MelanA) were used as control, and DCs electroporated with RNA encoding constitutively active IKKβ (caIKK) were used as case.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Xin Lai

PROVIDER: E-MTAB-9666 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Proteomic analysis reveals core monocyte-derived cell differentiation proteome and highlights cellular identity-specific proteins

Project description:Monocytes can give rise to multiple highly specialized cell types to perform a wide array of functions, ranging from pathogen phagocytosis to bone resorption. This differentiation is induced by the binding of cytokines to dedicated receptors on the surface of monocytes, which results in the initiation of genetic programs that enable cells to perform their specialized functions. Given their common background, it is not surprising that monocyte-derived cells share abilities and cellular markers, yet their specialized functions require a dedicated set of proteins. In order to dissect the monocyte differentiation process and to define cell type-specific marker proteins, we differentiated circulating monocytes into dendritic cells, M1 and M2 macrophages, and osteoclasts, and assessed their proteomes by quantitative mass spectrometry throughout the differentiation process. Statistical analysis indicated that monocyte differentiation is a linear process characterized by a common core of proteins that is similarly affected among the distinct differentiation paths. Throughout the specialization process a cluster of RNA-binding and processing proteins was downregulated whereas proteins associated to metabolic processes were increased. Analysis of the specialized cells after 10 days of differentiation uncovered existing and putative novel dendritic cell markers. Combined, we here present a comprehensive proteomic analysis of monocyte differentiation uncovering shared and distinct proteomic features of differentiating monocytes and monocyte-derived cells.

2021-09-09 | PXD016245 | Pride

Transcription profiling of human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level

Project description:Day 6 human monocyte derived dendritic cells were left unstimulated or matured for 2 days using the golden standard maturation cocktail currently used in clinical practice. Maturation induced changes in mRNA expression were determined by calculation of expression in mature DC relative to immature DC. Obtained gene expression raito's were compared to protein expression ratio's from the same batch of cells at the pathway level (proteomics data of this experiment is deposited in Human Proteinpedia, accession number pending).

2010-03-24 | E-MEXP-2290 | biostudies-arrayexpress

Transcription profiling by array of human dendritic cells after Poly(I:C)-based or PGE2-based maturation

Project description:Generation of human monocyte-derived DCs Peripheral blood mononuclear cells (PBMC) were isolated by Ficoll density centrifugation from buffy coats or whole blood of healthy donors and resuspended in serum-free medium (CellGro, CellGenix GmbH, Freiburg, Germany), supplemented with penicillin (50U/ml)/streptomycin (50?g/ml). Cells were plated at a density of 1-1,25 e6/cm2 in T-25 flasks and allowed to adhere for 2h at 37oC. Non-adherent cells were removed by washing twice with PBS and frozen as T cell source for stimulation experiments. Adherent monocytes were differentiated into immature DC with 1000U/ml GM-CSF and 50ng/ml IL-4 (""im DC""). Unless stated otherwise, cytokines were purchased from CellGenix GmbH, Freiburg, Germany. Cytokines were replenished on day 3. Maturation was achieved by incubation with either IL-1?; (10ng/ml), IL-6 (1000U/ml), TNF?; (10ng/ml) and PGE2 (1?g/ml, ICN, Aurora, Ohio, USA) (""PGE2-DC"") or IL-1?; (25ng/ml), IFN?; (3000U/ml, Schering-Plough, Brussels, Belgium), IFN?; (1000U/ml Strathmann Biotech AG), TNF?; (50ng/ml) and poly(I:C) (a synthetic, double-stranded RNA, 20ng/ml, Sigma-Aldrich, Taufkirchen, Germany) (""poly(I:C)-DC"") on day 6 for 48 hours Total RNA was isolated from DC before and after cytokine maturation

2008-11-01 | E-MEXP-1230 | biostudies-arrayexpress

Genomic expression analysis of human monocyte-derived DCs and monocytes

Project description:To identify the functional non-coding RNAs in human DC development, we explored the gene expression profiles during DC development from peripheral monocytes. Using RNA-seq, we identified many annotated lncRNAs with markedly altered expressions during human DC differentiation and maturation. RNA samples from human peripheral blood monocytes and monocyte-derived DCs were collected. RNAs from 3 donors were pooled together to form monocyte sample or DC sample and then these two samples were subjected to RNA-seq and analysis.

2014-05-02 | E-GEOD-54401 | biostudies-arrayexpress

Inhibition of p38 MAPK in DC progenitor cells endows DCs with superior immunogenicity

Project description:Analysis of the p38 MAPK pathway in regulation of dendritic cells (DCs) differentiation at the gene expression level. Bone marrow cells were cultured with mGM-CSF (20 ng/ml) in the presence of 1.5 mM of SB202190 or 0.1% DMSO. At day 7, semi-adherent cells were collected as immature DCs (iDCs). iDCs were matured by TNF-a (10 ng/ml) and IL-1b (10 ng/ml) for 48 hours. Results showed that p38 MAPK activity in DC progenitor cells acts as an antigen presentation attenuator, and disabling this critical brake during DC differentiation endows DCs with enhanced immunogenicity, which may be useful for the induction of antitumor immune responses. Total RNA was obtained from 2-day-cultured bone marrow cells, iDCs and mature DCs.

2014-05-22 | E-GEOD-57879 | biostudies-arrayexpress

microRNA expression signature of monocyte-derived dendritic cells (DCs) from peripheral blood mononuclear cells (PBMCs)

Project description:In order to detect the microRNA expression profile of in vitro generated dendritic cells , purified monocytes from PBMCs were used as dendritic cell (DCs) precursors and were cultured in medium with cocktail for differentiation and maturation to immature dendritic cells (iDCs) and mature dendritic cells (mDCs). microRNA samples were isolated from precursor, iDCs and mDCs and used for microarray-based microRNAs expression profiles. To generate enough amount of immature DC (iDCs) and mature DCs (mDCs), monocytes were differentiated with GM-CSF and rhIL-4 for 2 days and maturated in the presence of TNF-α, IL-1β, IL-6 and PGE2 for another 2 days. With the anticipation to insight developmental-stage-specific microRNAs with potential functions related to monocyte derived DCs, global microRNAs expression profiling was set using microarray technology.microRNA expression profiles were performed in triplicate independent experiments starting for 3 groups of precursor, iDC and mDC generated from different blood donors.

2013-01-28 | E-GEOD-15036 | biostudies-arrayexpress

Gene expression profiling of monocyte-derived dendritic cells (DCs) from peripheral blood mononuclear cells (PBMCs)

Project description:In order to detect the gene expression profile of in vitro generated dendritic cells , purified monocytes from PBMCs were used as dendritic cell (DCs) precursors and were cultured in medium with cocktail for differentiation and maturation to immature dendritic cells (iDCs) and mature dendritic cells (mDCs). Total RNA samples were isolated from precursor, iDCs and mDCs and used for microarray-based gene expression profiles. To generate enough amount of immature DC (iDCs) and mature DCs (mDCs), monocytes were differentiated with GM-CSF and rhIL-4 for 2 days and maturated in the presence of TNF-α, IL-1β, IL-6 and PGE2 for another 2 days. With the anticipation to insight developmental-stage-specific genes with potential functions related to monocyte derived DCs, global gene expression profiling was set using microarray technology.gene expression profiles were performed in triplicate independent experiments starting for 3 groups of precursor, iDC and mDC generated from different blood donors.

2013-01-28 | E-GEOD-15075 | biostudies-arrayexpress

Gene expression profile of HIF-1Î± silenced or non-silenced human DCs stimulated with A. fumigatus under normoxic or hypoxic conditions

Project description:DCs play a central role for the immune response against the mold Aspergillus fumigatus. Hypoxic microenvironments occur during infection with A. fumigatus. Hypoxia and signaling via hypoxia inducible factor 1Î± may modulate the response of DCs; however, the role in fungal infections is unclear. We used microarrays to determine the influence of hypoxia and HIF-1Î± signaling on the immune response of human DCs towards A. fumigatus. HIF-1Î± silenced or non-silenced, human monocyte-derived DCs were cultivated for 6 h in normoxia or hypoxia (1 % O2) without stimulation or stimulated with inactivated germ tubes of A. fumigatus. Three independent experiments with DCs derived from different blood donors were performed. RNA was extracted and hybridized on Affymetrix microarrays.

2015-11-01 | E-GEOD-60729 | biostudies-arrayexpress

Recombinant human lactoferrin activates human dendritic cells via Toll-like receptors-2 and -4

Project description:Talactoferrin alfa (TLF) is a unique recombinant version of human lactoferrin, an important immunomodulatory protein present in exocrine secretions and in the secondary granules of neutrophils. Talactoferrin has demonstrated anti-cancer activity in preclinical studies and in Phase III clinical trials in patients with Renal Cell Cancer and non-small cell lung cancer. We have shown that TLF induces the maturation of human DCs derived from monocytes, suggesting that the linkage of the innate and adaptive immunity through DC maturation is a key immune function mediated by TLF. In this study we used genome-wide expression analysis to explore the mechanisms by which TLF leads to the functional maturation of DC. We show that GMP level recombinant TLF activates human DCs in a Toll-like receptor (TLR) -2 and -4 dependent manner. Human peripheral blood mononuclear cells (PBMCs) were obtained from buffy coats of healthy donors. CD14+ cells were isolated from fresh PBMCs by positive immunoselection with magnetic beads. Immature dendritic cells (i-DC) from four donors were generated using granulocyte-macrophage colony-stimulating factor (GM-CSF) and IL-4. On day 6, cells were harvested in order to have iDC or mDC (conventionally matured DC) by addition of Tumor Necrosis Factor (TNF) -alfa and IL-1beta or TLF-DC (Talactoferrin matured DC) adding Food and Drug Administration-approved, GMP level recombinant TLF generated in eukaryotic cells. After 24 hour culture, cells were harvested and analyzed with Illumina arrays.

2013-12-30 | E-GEOD-26438 | biostudies-arrayexpress

MYB/miR4863p/MAF/ axis in hematopoietic progenitor cell fate decision

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-08-07 | E-GEOD-60301 | biostudies-arrayexpress