Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential gene expression in Aspergillus fumigatus induced by human platelets in vitro

ABSTRACT: Differentially expressed genes in Aspergillus fumigatus following exposure to human platelets in a timeseries experiment (15min, 30min, 1h, 3h) compared to untreated fungi as reference using customized Geniom (R) Biochips (febit) comprising 9500 genes (14051 features) were studied in order to gain a better understanding of the way platelets may affect Aspergillus spp. and contribute to antifungal host defense.

INSTRUMENT(S): Geniom RT Analyzer, Geniom

ORGANISM(S): Aspergillus fumigatus Af293

SUBMITTER: Hubert Hackl

PROVIDER: E-MTAB-3024 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Differential gene expression in Aspergillus fumigatus induced by human platelets in vitro.

Perkhofer Susanne S Zenzmaier Christoph C Frealle Emilie E Blatzer Michael M Hackl Hubert H Sartori Bettina B Lass-Flörl Cornelia C

International journal of medical microbiology : IJMM 20150117 3

Invasive aspergillosis is characterized by vascular invasion and thrombosis. In order to determine the antifungal activity of human platelets, hyphal elongation and metabolic activity of a clinical A. fumigatus isolate were measured. Genome-wide identification of differentially expressed genes in A. fumigatus was performed after exposure to platelets for 15, 30, 60 and 180 min. Data were analyzed by gene ontology annotation as well as functional categories (FunCat) and KEGG enrichment analyses. ...[more]

PMID: 25661519

Similar Datasets

Characterization of the lag-phase associated cold acclimation gene expression responses in L. monocytogenes EGD-e

Project description:Gene expression changes in L. monocytogenes EGDe during lag-phase associated cold acclimation were succesfully defined through expression profiling The gene expression profiles of L. monocytogenes EGD-e cells that underwent cold acclimation during lag phase were analyzed in a genome-wide microarray assay with a total of 2847 genes, were the resulting significantly regulated genes were splitted in two groups (up-and down-regulated)

2013-04-19 | E-GEOD-46182 | biostudies-arrayexpress

Platelet-secreted microRNA-223 promotes endothelial cell apoptosis induced by advanced glycation end products via targeting the insulin-like growth factor 1 receptor

Project description:Platelets contain abundant miRNAs, however, the biogenesis pathway of miRNAs in anucleate platelets is unclear. Platelet-rich plasma was diluted in washing buffer and the platelet suspension was centrifuged to isolated pure platelets.Finally, platelets were recovered in suspension buffer at the concentration of 4–5×10^8 platelets/ml. Aliquots of the platelet suspensions were activated in the presence of 2.5 mM CaCl2 with 0ng/ml or 1 ng/ml thrombopoietin (TPO)

2014-02-04 | E-GEOD-51453 | biostudies-arrayexpress

NanoString- Transcriptional profiling of LPS-primed and inflammasome-activated untouched, or platelet-depleted human CD14+ monocytes

Project description:The goal of this experiment was to explore how human platelets affect the transcriptional responses of primary human CD14+ blood monocytes to lipopolysaccharide (LPS), and NLRP3 activation with Nigericin. For this purpose, we analyzed the mRNA expression of 770 myeloid-specific transcripts using the nCounter® Nanostring Human Myeloid Innate Immunity Panel v2. We isolated classical monocytes (CD14+CD16−) from the peripheral blood of healthy volunteers. Monocytes were derived from PBMCs using negative selection with the EasySep™ Human Monocyte Isolation Kit from STEMCELLTM Technologies. We modified this process by either including or excluding a platelet-depleting cocktail, creating two groups: \\"Standard Monocytes (StdMo)\\" and \\"Platelet-depleted Monocytes (PdMo).\\" To examine the impact of platelets further, we supplemented PdMos with fresh autologous platelets at a ratio of 50 platelets per monocyte, resulting in a third group, \\"PdMo + Plts.\\" StdMos were prepared according to the standard protocol provided by the EasySep™ Kit. For the PdMos, a Platelet Removal Component (50 µl ml−1) from the kit was used during isolation. We also reconstituted platelet-depleted monocytes with platelets and analyzed platelets alone to determine their specific mRNA contributions. The groups—StdMo, PdMo, PdMo + Plts, and platelets alone—were then exposed to 2 ng/ml of Ultrapure LPS (from E. coli O111:B4) for 4.5 hours, or stimulated with LPS for 3 hours followed by inflammasome activation with Nigericin (10 µM) for 90 min before extracting RNA for analysis.

2024-05-31 | E-MTAB-14072 | biostudies-arrayexpress

Platelet transcriptome profile

Project description:Transcriptional profiling of platelets from patients with premature atherosclerosis and matched controls

2011-07-07 | E-MTAB-710 | biostudies-arrayexpress

Platelet microRNA expression profiles of acute coronary syndrome patients with high and low platelet reactivity

Project description:To explore the diverse platelet microRNA (miRNA) expression between high platelet reactivity (HPR) and low platelet reactivity (LPR) patients with acute coronary syndromes (ACS), we enrolled a cohort of ACS patients and performed miRNA expression profiling of platelets from four HPR and four LPR patients using human miRNA microarray system. VerifyNow P2Y12 assay was applied to indentify HPR and LPR. Venous blood was drawn from the patients and was centrifuged to prepare platelets. Among the candidate differentially expressed miRNAs, miR-15b expression was further confirmed to be lower in platelets of 22 HPR patients than 17 LPR by quantitative reverse-transcription polymerase chain reaction (RT-qPCR). We enrolled a consecutive cohort of 290 ACS patients and assessed the platelet reactivity using VerifyNow P2Y12 assay. In this study, HPR was defined as M-bM-^IM-%300 platelet reactivity unit (PRU) while LPR <170 PRU. miRNA microarray analysis was performed in platelets of four HPR and four LPR patients with ACS.

2014-07-17 | E-GEOD-59488 | biostudies-arrayexpress

Transcriptome profiling of human ovarian cancer cell lines grown in the presence and absence of washed human platelets

Project description:The objective of the study was to determine the influence of platelets on the transcriptome profile of ovarian cancer cells Ovarian cancer cell lines (SKOV3 and 59M) were co-cultured with human washed platelets for 24 hours prior to RNA extraction. These samples were then analysed on affymetrix human Gene 2.0ST arrays.

2022-07-01 | E-MTAB-9673 | biostudies-arrayexpress

Long-term adaptation to hypoxic conditions - Febit transcriptome analysis

Project description:Aspergillus fumigatus is an opportunistic, airborne pathogen causing invasive aspergillosis in immunocompromised patients. During the infection process A. fumigatus is challenged by hypoxic microenvironments occurring in inflammatory, necrotic tissue. To gain further insights into the adaptation mechanism, A. fumigatus was cultivated in an oxygen-controlled chemostat under hypoxic and normoxic conditions. Transcriptome analysis revealed significant increases in transcripts associated with cell wall polysaccharide metabolism, amino acid and metal ion transport, nitrogen metabolism and glycolysis. A concomitant reduction in transcript levels was observed with cellular trafficking and G-protein coupled signaling. To learn more about the functional roles of hypoxia-induced transcripts we deleted A. fumigatus genes putatively involved in reactive nitrogen species detoxification (fhpA), NAD+ regeneration (frdA, osmA) nitrogen metabolism (niaD, niiA) and respiration (rcfB). We show that the NO-detoxifying flavohemoprotein fhpA is strongly induced by hypoxia independent of the nitrogen source, but is dispensable for hypoxic survival. By deleting the nitrate reductase gene niaD, the nitrite reductase gene niiA and the two fumarate reductases genes frdA and osmA, we found that alternative electron acceptors such as nitrate and fumarate do not have a significant impact on growth of A. fumigatus during hypoxia, but that functional mitochondrial respiratory chain complexes are essential under these conditions. Inhibition studies indicated that primarily complex III and IV play a crucial role in the hypoxic growth of A. fumigatus.

2014-07-01 | E-MTAB-2699 | biostudies-arrayexpress

RNA-Seq of human platelet polyA-mRNA from a normal male

Project description:RNA-sequencing analysis of human platelet polyA-mRNA from a normal male. The goal of this experiment was to identify genes expressed in unstimulated circulating platelets.

2012-06-30 | E-MTAB-715 | biostudies-arrayexpress

Functionally-relevant splicing of resident pre-mRNAs in anucleate platelets upon activation by physiological stimuli

Project description:Platelet activation is the key event triggering thrombus formation in physiological and pathological conditions, such as acute coronary syndromes. Current therapies using antiaggregants still fail to prevent thrombotic coronary events in a significant number of patients, indicating that the mechanisms modulating platelet response during activation need to be clarified. The evidence that platelets are capable of de novo protein synthesis in response to stimuli raised the issue of how the activity of megakaryocyte-derived mRNAs is regulated in these anucleate cell fragments. We applied a combined multi-omics approach to investigate this phenomenon in platelets from healthy donors activated in vitro with Collagen or Thrombin Receptor Activating Peptide. Combining HiRIEF LC-MS to transcriptome analysis by RNA-Seq allowed platelet proteome characterization at deep coverage, revealing a significant effect of either stimulus on proteome composition. In silico intron retention analysis was then applied to search for splicing events induced by platelet activation, coupled to unbiased proteogenomics, to correlate intron retention in resting platelets to intron removal by RNA splicing during activation. This allowed identification of a set of transcripts, specifically involved in platelet shape changes, showing reduced intron retention and high peptide representation at exon-exon junctions in activated vs resting platelets. These results indicate that RNA splicing events takes place in platelets during activation and that pre-mRNA maturation of specific transcripts is part of the activation cascade and could therefore provide novel molecular markers of platelet activation status in acute coronary syndromes and other pathological conditions.

2018-01-15 | E-MTAB-6148 | biostudies-arrayexpress

Platelets direct monocytes differentiation into multinucleated giant foam cells with suppressive response to mycobacterial stimulus

Project description:Co-culture of platelets with monocytes induces the forming of multinucleated giant foam cells (MP-Mac or MP-MNGCs). Compared with normal monocyte differentiated macrophages (M-Mac), the MP-MNGCs can engulf more mycobacteria with suppressed inflammatory responses (releasing more IL-10 with less TNF-gamma). Microarray analysis demonstrated that the MP-MNGCs greatly up-regulated CXCL5, PPBP, NT5E, PDPN, CXCL3 and other M2 related genes, such as ARG1, CXCL1, CD163, etc. GO analysis revealed higher cluster of genes in response to wounding and nuclear division. Immunohistochemistry studies indicated similar high expression of IL-10, CXCL5, CXCL3, PDPN and ARG1 expression in MNGCs of TB granuloma, which indicated that phagocytosis of activated platelets by monocytes might be involved in pathogenesis of TB granuloma. Microarray experiments were performed as dual-color hybridizations. To compensate for dye-specific effects, a dye-reversal color-swap was applied. Quality control and quantification of total RNA amount was assessed using an Agilent 2100 bioanalyzer (Agilent Technologies) and a NanoDrop 1000 spectrophotometer (Kisker).

2014-01-01 | E-GEOD-45960 | biostudies-arrayexpress

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