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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Comparison of DEV infected CEF with control

ABSTRACT: Duck enteritis virus (DEV) is an important herpesvirus pathogen of waterfowl associated with an acute, highly contagious lethal disease. Using a deep sequencing approach on RNA from infected chicken embryo fibroblast (CEF) cultures, we determined the global changes in the microRNA (miRNA) expression profiles during DEV infection. In addition to the changes in the expression of a number of host miRNAs as a result of DEV infection, we identified several novel DEV-encoded miRNAs. Unlike most Mardivirus-encoded miRNAs, the majority of the DEV miRNAs were encoded within the unique long region of the viral genome. The precursors of DEV miR-D18 and miR-D19 overlapped with each other suggesting similarities to miRNA-offset RNAs, although only the DEV-miR-D18-3p was functional in reporter assays. Identification of these novel miRNAs will add to the growing list of virus-encoded miRNAs enabling the exploration of their roles in pathogenesis. Each microRNA is spotted on the array 6 times. We compared expression of duck enteritis virus (DEV)-infected chicken embryo fibroblasts (CEF) with CEF control.

ORGANISM(S): Gallus gallus

SUBMITTER: Michael Watson

PROVIDER: E-GEOD-36258 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Comparison of DEV infected CEF with control

Project description:Duck enteritis virus (DEV) is an important herpesvirus pathogen of waterfowl associated with an acute, highly contagious lethal disease. Using a deep sequencing approach on RNA from infected chicken embryo fibroblast (CEF) cultures, we determined the global changes in the microRNA (miRNA) expression profiles during DEV infection. In addition to the changes in the expression of a number of host miRNAs as a result of DEV infection, we identified several novel DEV-encoded miRNAs. Unlike most Mardivirus-encoded miRNAs, the majority of the DEV miRNAs were encoded within the unique long region of the viral genome. The precursors of DEV miR-D18 and miR-D19 overlapped with each other suggesting similarities to miRNA-offset RNAs, although only the DEV-miR-D18-3p was functional in reporter assays. Identification of these novel miRNAs will add to the growing list of virus-encoded miRNAs enabling the exploration of their roles in pathogenesis.

2012-03-08 | GSE36258 | GEO

Transcriptome Analysis of Duck Spleen Infected by Duck enteritis virus

Project description:Purpose:To understand the transcriptome regulator of duck spleen infected with duck enteritis virus (DEV).Methods:50-day-old ducks were inoculated with 100 titer (The TCID50 of DEV was 10-9/0.1mL) and 10-2 titer two different viral titer of DEV in leg muscle for different durations (66 h, 90 h and 114 h) and seronegative control (0 h) were analyzed using next-generation RNA sequencing.Furthermore, the data were validated using quantitative real-time PCR.Results:There were 534, 685 and 580 genes differentially expressed in 100 titer, moreover, 511, 485 and 531 differentially expressed genes (DEGs) were obtained from 10-2 titer for 66 h, 90 h and 114 h, respectively. These genes were mainly involved in functional categories including immune response, extracellular space, heparin binding, oxygen transport, extracellular region, cellular response to interleukin-4, MHC class II protein complex, antigen processing and presentation of peptide or polysaccharide antigen via MHC class II, and pathways such as ribosome, ECM-receptor interaction, cell adhesion molecules, JAk-STAT signaling pathway, PPAR signaling pathway, neuroactive ligand-receptor interaction, phagosome.Conclusions: Different titers of DEV infection can stimulate different biological processes and signaling pathways in the spleen, and regulated the complex biological processes, metabolic and signaling pathways in the process of DEV infection.This transcriptome analysis of duck spleen infected with DEV in different time points is reported for the first time, it laid the foundation for further understanding of interactions between DEV and duck spleen tissue, molecular mechanisms of duck defend against DEV infection, and screening key functional genes.

2020-06-27 | GSE100524 | GEO

Circulating miRNAs as novel marker of pulmonary hypertension

Project description:We determined pattern of miRNAs of mild-to-severe human pulmonary arterial hypertension and compared the with health controls using microarray and subsequently validated by QPCRs Manuscript Title: Circulating miRNAs as novel marker for pulmonary hypertension. (Under Revision Plos One Manuscript ID: PONE-D-12-38535) Performed microRNA microarray from one healthy and one severe PH patient and compared the results using additional samples by qPCR for other miRNAs

2013-11-01 | E-GEOD-44145 | biostudies-arrayexpress

miRNA expression data from embryonic ureteric bud (UB) cells

Project description:UB cells FACS sorted from E15.5 mouse kidneys were analyzed for miRNAs expression. E15.5 UB cells FACS sorted from Rosa26YFP; Hoxb7Cre mice, total RNAs including miRNAs were purified and used for miRNA microarray

2014-08-28 | E-GEOD-60845 | biostudies-arrayexpress

Viral microRNA expression in two nasal NK T cell lymphoma cell lines

Project description:We have used microarray profiling to examine the expression of viral microRNAs (miRNAs) in two independently derived nasal natural killer T cell lymphoma (NKTCL) cell lines, SNK6 and SNT16. The goal of the study was to investigate the role of the viral miRNAs in the genesis and maintenance of NKTCLs. This experiment includes a total of 2 samples, one from SNK6 cells and the other from SNT16 cells.

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Roles for ATF6-regulated miRNAs in the ER stress response

Project description:We wished to determine the effects of activating the transcription factor, ATF6, on global miRNA expression. We utilized transgenic mice with a conditionally tamoxien-responsive form of ATF6 and assessed cardiac lysates from NTG and TG mice, both treated with tamoxifen and untreated, in order to identify differentially expressed miRNAs. We then focused on miRNAs of interest as well as the genes they are predicted to regulate. Four sample groups were assessed for miRNA expression: non-transgenic (NTG) mice treated with vehicle, NTG mice treated with tamoxifen, ATF6 transgenic (TG) mice treated with vehicle, and TG mice treated with tamoxifen

2012-01-02 | E-GEOD-33515 | biostudies-arrayexpress

miRNA-mediated post-transcriptional regulation of gene expression in ABR17 transgenic Arabidopsis thaliana under salt stress

Project description:Micro RNAs (miRNAs) are a class of small endogenous RNAs conserved in eukaryotic organisms including plants. They suppress gene expression post-transcriptionally in many different biological processes. Previously, we reported salinity-induced changes in gene expression in transgenic Arabidopsis thaliana plants that constitutively expressed a pea abscisic acid-responsive (ABR17) gene. In the current study, we used a microarray to investigate the role of miRNA-mediated post-transcriptional gene regulation in these same transgenic plants in the presence and absence of salinity stress. We identified nine miRNAs that were significantly modulated due to ABR17 gene expression, and seven miRNAs that were modulated in response to salt stress. The target genes regulated by these miRNAs were identified using starBase (sRNA target Base) Degradome analysis and through 5' RNA Ligase Mediated-Rapid Amplification of cDNA Ends (RLM-RACE). Our findings revealed miRNA:mRNA interactions comprising regulatory networks of Auxin Response Factor (ARF), ARGONAUTE 1, (AGO1), Dicer-like proteins 1 (DCL1), Squamosa Promoter Binding (SPB), NAC, APETALA 2 (AP2), Nuclear Factor-Y (NFY), RNA binding proteins, Arabidopsis thaliana vacuolar phyrophosphate 1 (AVP1) and Pentatricopetide repeat (PPR) in ABR17 transgenic A. thaliana, which control physiological, biochemical and stress signalling cascades due to the imposition of salt stress. Our results are discussed within the context of the effect of the transgene, ABR17, and the roles miRNA expression may play in mediating plant responses to salinity. In this miRNA-microarray experiment, a total of 4 samples were analyzed with their 3 biological replicates. Two samples, WT and ABR17 control (without salt treatment), were used as reference controls.

2014-01-31 | E-GEOD-53783 | biostudies-arrayexpress

Role of miRNAs in the differentiation of human embryonic stem cells to an endothelial cell lineage

Project description:To assess changes in the miRNA-ome during the early stages of endothelial differentiation, the expression of mature human miRNAs at days 2, 4 and 10 of endothelial differentiation (vs pluripotent time-matched samples) in SA461 hESC cell line was analysed in a two-channel microarray. Expression of the pluripotency-associated miRNAs miR-302a – d and miR-372 and miR-373 was significantly suppressed with progression of differentiation. The expression of miR-99b, miR-181a and miR-181b was, in contrast, increased in a time- and differentiation-dependent manner compared to time-matched pluripotent samples. The expression profiles were validated and good concordance was observed between microarray, Q-PCR and Northern blot analysis. This experiment includes a total of 28 samples which are divided in to 3 groups, each with 4 biological repeats: group 1, Parental pluripotent hESC control sample. group 2, time-matched pluripotent hESC control samples. Group 3, hESC cells directed toward endothelial differentiation at time points 2 days, 4 days and 10 days.

2012-01-01 | E-GEOD-33675 | biostudies-arrayexpress

Role of miRNAs in the neurogenesis of human neural stem cells

Project description:by use of the model of human embryonic stem cell (hESC)-derived neurogenesis, miRNAs involved in the differentiation from neural stem cells (hNSC) to neurons were profiled and identified. HNSC were differentiated into the neural lineage, out of which the neuronal subset was enriched through cell sorting based on select combinatorial biomarkers: CD15-/CD29Low/CD24High. This relatively pure and viable subpopulation expressed the neuronal marker alpha III-tubulin. The miRNA array demonstrated that a number of miRNAs were simultaneously induced or suppressed in neurons, as compared to hNSC. Real-time PCR further validated the decrease in levels of miR214, but increase in brain-specific miR7 and miR9 in the derived neurons. This experiment includes a total of 6 samples which are divided in to 2 groups, each with 3 biological repeats: 3 untreated normal samples as controls and 3 differentiated samples as the treated condition

2012-03-01 | E-GEOD-30572 | biostudies-arrayexpress

MicroRNA profiling of adult male zebrafish exposed to 17-beta estradiol (E2) for 0, 1, 4. 12 and 24 hours

Project description:Microarrays displaying zebrafish miRNAs specific probes were hybridized using RNA samples originating from whole body homogenates of male zebrafish exposed to 17-beta estradiol (E2) for 0, 1, 4. 12 and 24 hours. 0 hr fish No. 40, 41, 42. 1hr fish No. 8, 10, 11. 4hr fish No. 19, 20, 23. 12hr fish No. 24, 25, 26. 24hr fish No. 29, 31, 32. <br><br> The hybridizations used in these experiments: Chip 1: 10-42, Chip 2: 40-8, Chip 3: 41-11, Chip 4: 42-19, Chip 5: 20-40, Chip 6: 23-41, Chip 7: 25-42, Chip 8: 40-24, Chip 9: 41-26, Chip 10: 42-29, Chip 11: 31-40, Chip 12: 32-41

2007-12-30 | E-MEXP-1147 | biostudies-arrayexpress

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