Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microarray of human primary CD16+ monocytes treated with fractalkine (CX3CL1) against untreated controls

ABSTRACT: This experiment is a part of the larger study on angiotensin II role in the upregulation of the CX3CL1 expression and its release in human first trimester placenta. CX3CL1 (or fractalkine) is chemokine involved in the pathogenesis of hypertension, which can be secreted by trophoblasts, initiating the cross talk with monocytes. Thus, we performed the microarray experiment to study the effects of recombinant human CX3CL1 on the transcriptome of human primary monocytes.

INSTRUMENT(S): GeneChip® Scanner 3000 7G

ORGANISM(S): Homo sapiens

SUBMITTER: Alina Frolova

PROVIDER: E-MTAB-7484 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Full transcriptome analysis of MCF-7 cells treated with screening hit compounds versus control

Project description:This experiment was performed as part of a hit screening project. Transcriptome analysis was performed to determine whether the screened hits induced a gene expression pattern consistent with proteasome inhibition. MCF-7 cells were exposed to 2x[IC50] of hit compounds for six hours. RNA was processed according to manufacturer's protocol for preparation of HuGene 2.0ST chips to acquire biotinylated sense-strand DNA. Biotinylated DNA was hybridized to HuGene 2.0ST chips at 37°C for 16 hours in a GeneChip® Hybridization Oven 645, washed and stained using the GeneChip® Fluidics Station 450 using the FS450_0002 protocol and scanned with a GeneChip® Scanner 3000 7G.

2018-08-04 | E-MTAB-7024 | biostudies-arrayexpress

Characterization of human pluripotent stem cell-derived hepatocytes with adult features and potential for modeling metabolic diseases

Project description:Liver disease and toxicity that causes impaired liver functionality have severe effects on normal body functions. There is a strong need for better and more predictable in vitro models for studying disease and improving mechanistic understanding of adverse effects of drugs in humans. This experiment aimed to characterize human induced pluripotent stem cell-derived hepatocytes (hiPS-HEP), in order to assess their potential as in vitro tools for metabolism studies and disease modeling. hiPS-HEP from three cell lines were compared to human primary hepatocytes from three donors, before and after plating.

2020-02-06 | E-MTAB-8286 | biostudies-arrayexpress

Site-specific protein modification by 3-n-butylphthalide in primary hepatocytes: covalent protein adducts diminished by glutathione and N-acetylcysteine

Project description:The toxicity of NBP and its four major metabolites were compared in both PHHs and PRHs, and 3-OH-NBP was found to be the most toxic metabolite. 3-OH-NBP induced remarkable cell death and oxidative stresses in hepatocytes, which correlated well with the levels of glutathione and N-acetylcysteine adducts (3-GSH-NBP and 3-NAC-NBP) in cell supernatants. Additionally, 3-OH-NBP covalently conjugated with intracellular Cys, Lys and Ser, with preferable binding to Cys sites at Myh9 Cys1380, Prdx4 Cys53, Vdac2 Cys48 and Vdac3 Cys36. Furthermore, we found that CYP3A4 induction by rifampicin augmented NBP-induced cell toxicity and supplementing with GSH or NAC alleviated the oxidative stresses and reactive metabolites caused by 3-OH-NBP.

2022-10-22 | PXD029480 | Pride

Transcriptomic characterization of classical monocytes highlights the involvement of immuno-inflammation in bone erosion in Rheumatoid Arthritis

Project description:Rheumatoid arthritis (RA) is a chronic inflammatory disease associated with localized bone involvement characterized by the presence of bone erosions. Evidence-based data suggest that under inflammatory conditions, classical monocytes are the main source of osteoclasts and might be involved in bone erosion pathophysiology. Here, we analyze the transcriptomic profile of classical monocytes in erosive and non-erosive rheumatoid arthritis patients in order to better understand their contribution to bone erosion. Thirty-nine premenopausal RA patients and 20 healthy age-matched women were recruited for this study. Classical monocytes were isolated from peripheral blood through negative selection. Sequencing library was constructed using the Quant-seq® 30 mRNA-Seq Library Prep Kit (Lexogen®) and sequenced using an Illumina Seq 2500 platform (Illumina®). Differential expression analysis was performed between patients and control groups. Therefore, gene sets analysis was performed to identify the enriched biological pathways. Results suggested that alterations in pathways related to the inflammatory process and impairment of bone formation have an important role in the pathophysiology of bone erosions in patients with rheumatoid arthritis.

2023-09-19 | E-MTAB-13361 | biostudies-arrayexpress

Transcriptomic Signatures of Classical Monocytes Reveal Pro-Inflammatory Modules and Heterogeneity in Polyarticular Juvenile Idiopathic Arthritis

Project description:Polyarticular Juvenile Idiopathic Arthritis (pJIA) is a childhood-onset autoimmune disease. Immune cells contribute to persistent inflammation observed in pJIA. Despite the crucial roleof monocytes in arthritis, the precise involvement of classical monocytes in the pathogenesis of pJIA remains uncertain. Here, we aimed to uncover the transcriptomic patterns of classical monocytes in pJIA, focusing on their involvement in disease mechanism and heterogeneity. Seventeen healthy subjects and eighteen premenopausal women with pJIA according to ILAR criteria were included. Classical monocytes were isolated and RNA sequencing was performed. Differential expression analysis was used to compare pJIA patients and healthy control group. Differentially expressed genes (DEGs) were identified and gene set enrichment analysis (GSEA) was performed. Using unsupervised learning approach, patients were clustered in two groups based on their similarities at transcriptomic level. Subsequently, these clusters underwent a comparative analysis to reveal differences at the transcriptomic level. We identified 440 DEGs in pJIA patients of which 360 were up-regulated and 80 down-regulated. GSEA highlighted TNF- and IFN- response. Importantly, this analysis detected genes targeted by pJIA therapy, but also identified new modulators of immuno-inflammation. PLAUR, IL1B, IL6, CDKN1A, PIM1 and ICAM1 were pointed as drivers of chronic hyperinflammation. Unsupervised learning approach revealed two clusters within pJIA, each exhibiting varying inflammation levels. These findings indicate the pivotal role of immuno-inflammation driven by classical monocytes in pJIA and reveals the existence of two subclusters within pJIA, regardless the positivity of rheumatoid factor and anti-CCP, paving the way to precision medicine.

2024-05-06 | E-MTAB-14035 | biostudies-arrayexpress

Immune and HCT116 RNA mixtures

Project description:These experiments were designed as a benchmark tool for deconvolution methods. 5 immune cell populations were sorted from 3 healthy donors' peripheral bloods. Peripheral Blood Mononuclear Cells (PBCMs) and PolymorphoNuclear Cells (PMN) were separated using gradient centrifugation. T cells (DAPI-/CD3+/CD14-/CD19-/CD56-), monocytes (DAPI-/CD3-/CD14+/CD19-/CD56-), B cells (DAPI-/CD3-/CD14-/CD19+/CD56-) and NK cells (DAPI-/CD3-/CD14-/CD19-/CD56+) were FACS-sorted from PBMCs and neutrophils (DAPI-/CD66b+/CD19-/CD3-/CD56-/CD14-) were sorted from PMNs. RNA was extracted from the purified cell population, as well as from the HCT116 colon cancer cell line. RNAs from pure populations were then mixed in various proportions. RNA from HCT116 cells and FACS-sorted T cells (DAPI-/CD3+/CD14-/CD19-/CD56-), monocytes (DAPI-/CD3-/CD14+/CD19-/CD56-), B cells (DAPI-/CD3-/CD14-/CD19+/CD56-), NK cells (DAPI-/CD3-/CD14-/CD19-/CD56+), and neutrophils (DAPI-/CD66b+/CD19-/CD3-/CD56-/CD14-) were mixed in various proportions.

2016-02-18 | E-GEOD-64385 | biostudies-arrayexpress

Transcription profiling of human early and late pubertal females reveals a brief bout of exercise alters gene expression and distinct gene pathways in PBMC

Project description:We compared PBMC genomic response to exercise in both early (EG) and late-pubertal girls (LG) Experiment Overall Design: Twenty healthy females (age range 8-17 y/o) participated in this study. A blood sample was taken before the onset of exercise and immediately after 30-min exercise bout. PBMCs were isolated using OptiPrep® Density Gradient Medium (SIGMA). Total RNA was extracted using TRIzol®. cRNA was hybridized onto Affymetrix U133+2 arrays (total of 40 chips).

2009-06-26 | E-GEOD-14642 | biostudies-arrayexpress

LPS stimulation of human PBMC-derived macrophages

Project description:Immunoresponsive gene 1 (IRG1) is one of the highest induced genes in macrophages under pro-inflammatory conditions and its function has been recently described: it codes for immune-responsive gene 1 protein/cis-aconitic acid decarboxylase (IRG1/CAD), an enzyme catalyzing the production of itaconic acid from cis-aconitic acid, a tricarboxylic acid (TCA) cycle intermediate. Itaconic acid possesses specific antimicrobial properties inhibiting isocitrate lyase, the first enzyme of the glyoxylate shunt, an anaplerotic pathway that bypasses the TCA cycle and enables bacteria to survive on limited carbon conditions. To elucidate the mechanisms underlying itaconic acid production through IRG1 induction in macrophages, we examined the transcriptional regulation of IRG1. Using a combination of literature information, transcription factor prediction models and genome-wide expression arrays, we inferred the regulatory network of IRG1 in mouse and human macrophages. 3 unstimulated (Control) and 3 LPS-stimulated human PBMC-derived macrophages

2016-02-25 | E-GEOD-76561 | biostudies-arrayexpress

RNA-seq expression profiling of NPM1mutated normal-AML with methylome status for HIST1 gene, i.e. H3K27me3 high (N=16) and H3K27me3 low (N=11). Transcriptome was done with Affymetrix HG-133+2.0 and Affymetrix Human Gene 2.0 ST microarrays

Project description:The epigenetic machinery is frequently altered in acute myeloid leukemia (AML). Focusing on cytogenetically normal (CN) AML, we previously described an abnormal H3K27me3 enrichment covering 70 kb on the HIST1 cluster (6.p22). Here, we further investigate the molecular, functional, and prognosis significance of this epigenetic alteration in NPM1-mutated (NPM1mut) CN-AML. H3K27me3 HIST1high group of patients

2020-08-25 | E-MTAB-6997 | biostudies-arrayexpress

miRNA profile of macrophage from different TB patients

Project description:the microRNA profiles of the host macrophages were studied by microarray in a small cohort with active MTB disease, latent infection (LTBI), and from healthy controls. From each individual in the three cohorts: the healthy (n=3), the latent (n=4), and the active TB patients (n=3), whole blood specimens were collected for monocytes isolation. Monocytes were induced into macrophage in vitro and total RNA were extracted for miRNA profiles analysis.

2015-07-01 | E-GEOD-65810 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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