Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Interaction between ROS and miR-451

ABSTRACT: Reactive Oxygen Species (ROS) could be a stress factor that affects microRNA regulation and function in macrophages. The production of microRNAs (miRNA) is influenced by various stimuli, including environmental stresses. We hypothesized that ROS-associated stress could regulate macrophage miRNA synthesis. p47phox-/- mice have deficient NADPH oxidase activity resulting in decreased ROS production. We cultured bone marrow-derived macrophages (BMDM) from wild type (WT) and p47phox-/- mice and profiled miRNA expression using microarrays. The microarray data reveals that there are differences in the expression levels of different miRs, and our studies suggest functional crosstalk between ROS and miR-451 in the regulation of macrophage oxidant stress. Mouse bone marrow-derived macrophages (BMDMs) were obtained from WT (wild type) and p47phox-/- mice. MicroRNAs were isolated by using the mirVana miRNA kit, and a TaqMan rodent microRNA array (consisting of Megaplex RT Primers, Rodent Pool-A, Applied Biosystems) was used for microarray. The array enables quantitation of the expression levels of up to 380 microRNAs and controls. Rodent Pool A contains reverse transcription (RT) primers for 335 and 238 unique microRNAs for mouse and rat, respectively, plus 4 species-specific controls. The data were analyzed on RQ manager software (Qiagen, SA Biosciences) and normalized to the endogenous controls, and analyzed for fold change of miRs in WT compared to p47phox-/-.

ORGANISM(S): Mus musculus

SUBMITTER: Ravi Ranjan

PROVIDER: E-GEOD-55189 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

microRNA profiling of multiple myeloma bone marrow

Project description:Bone marrow microenvironment in MM contains a unique miR signature, which is partially present and detectable in the peripheral blood. A subset of miRs (let-7i, miR-106b, miR-15a, and miR16) shows aberrant expression in the precursor lesion of MGUS, while aberrant expression of other miRs (let-7a, miR-15a/b, miR-19b, miR-20a, miR-21, miR-223, and miR-361) is associated with cell proliferation and disease progression. miRNA profiling was performed using Agilent miRNA array platforms with RNAs isolated from the bone marrow supernatant of multiple myeloma.

2016-07-01 | E-GEOD-49261 | biostudies-arrayexpress

microRNA profiling in pediatric AML

Project description:MicroRNAs (miRNAs) play a pivotal role in the regulation of hematopoiesis and development of leukemia. Great interest emerged in modulating miRNA expression for therapeutic purposes. In order to identify miRNAs, which specifically suppress leukemic growth of AML with t(8;21), inv(16) or MLL-rearrangement by inducing differentiation, we conducted a miRNA expression profiling in a cohort of 90 cytogenetically characterized, de novo pediatric AML cases. Four miRNAs, specifically downregulated in MLL-rearranged, t(8;21) or inv(16) AMLs, were characterized by their tumor suppressive properties in cell lines representing those respective cytogenetic groups. Among those, forced expression of miR-9 reduced leukemic growth and induced monocytic differentiation of t(8;21) AML cell lines in vitro and in vivo. The tumor suppressive functions of miR-9 were specifically restricted to AML cell lines and primary leukemic blasts with t(8;21). On the other hand, these functions were not evident in AML blasts from patients with MLL-rearrangements. We showed that miR-9 exerts its effects through the cooperation with let-7 to repress the oncogenic LIN28B/HMGA2 axis. Thus, miR-9 is a tumor suppressor-miR which acts in a stringent cell context-dependent manner. In order to identify miRNAs, which specifically suppress leukemic growth of AML with t(8;21) (n=21), inv(16) (n=17) or MLL-rearrangement (n=35) by inducing differentiation, we conducted a miRNA expression profiling in a cohort of 90 cytogenetically characterized, de novo pediatric AML cases, which also included 12 t(15;17) and 5 t(7;12) samples.

2014-01-01 | E-GEOD-52541 | biostudies-arrayexpress

Interaction between ROS and miR-451

Project description:Reactive Oxygen Species (ROS) could be a stress factor that affects microRNA regulation and function in macrophages. The production of microRNAs (miRNA) is influenced by various stimuli, including environmental stresses. We hypothesized that ROS-associated stress could regulate macrophage miRNA synthesis. p47phox-/- mice have deficient NADPH oxidase activity resulting in decreased ROS production. We cultured bone marrow-derived macrophages (BMDM) from wild type (WT) and p47phox-/- mice and profiled miRNA expression using microarrays. The microarray data reveals that there are differences in the expression levels of different miRs, and our studies suggest functional crosstalk between ROS and miR-451 in the regulation of macrophage oxidant stress.

2014-07-09 | GSE55189 | GEO

In silico analyses of survival-associated microRNA signatures in pediatric osteosarcoma

Project description:Osteosarcoma is the most common bone tumor in children, adolescents, and young adults. In contrast to other childhood malignancies, no biomarkers have been consistently identified as predictors of outcome. This study was conducted to assess the microRNAs (miRs) expression signatures in pre-treatment osteosarcoma specimens and correlate with outcome to identify biomarkers for disease relapse The cohort consisted of 25 patients of 70% Mexican-American ethnicity. High-throughput RT-qPCR approach was used to generate quantitative expression of 754 miRs in the human genome.

2016-03-22 | E-GEOD-79181 | biostudies-arrayexpress

miRNA profiling array and analysis in mouse hippocampal neurons

Project description:We addressed the potential for global regulation of miRNA biogenesis by BDNF using miRNA arrays that selectively measure mature miRNA, as opposed to pre-miRNA. Hippocampal neurons were treated with BDNF for 30 min in the presence of Actinomycin-D to assess changes due to processing of existing pre-miRNAs rather than new pre-miRNA production. We used Applied Biosystems 7900HT Fast Real-Time PCR system using Taqman Rodent MicroRNA Array A. Data is from three paired BDNF and Mock experiments (1,2,3). Each array (TaqMan) contained 375 rodent miRNA targets of which 195 were detectable in hippocampus in three independent paired experiments.

2012-03-02 | E-GEOD-35969 | biostudies-arrayexpress

Global microRNA profiling of the mouse ventricles during development of severe hypertrophic cardiomyopathy and heart failure

Project description:The study sought to determine the global miRNA profile of ventricles during early and end-stage hypertrophic cardiomyopathy in a severe double mutant mouse model of the disease. MicroRNA expression profiles of ventricles of transgenic mice with a mutation in both the myosin heavy chain gene (MYH7 Arg403Gln) and cardiac troponin I gene (TNNI3 Ser203Gln) and of non-transgenic mice were determined using Rodent TaqMan Low Density miRNA Arrays A v2.0 (TLDA, Life Technologies). MicroRNA profiles were measured at 10 days of age and 16 days of age, in 3 biological replicates. qRT-PCR analysis of microRNAs of ventricles of three transgenic mice and three non-transgenic mice age 10 days, and three transgenic mice and three non-transgenic mice age 16 days. 450 ng RNA was reverse transcribed, without pre-amplification, using TaqMan MicroRNA Reverse Transcription Kit and Megaplex RT Primers rodent pool A (Life Technologies). Complementary DNA (cDNA) was amplified using a TaqMan rodent microRNA A Array v2.0 (Life Technologies) with TaqMan Universal PCR Master Mix on an ABI 7900HT Sequence Detection System.

2012-05-11 | E-GEOD-37692 | biostudies-arrayexpress

Mouse Mast Cell

Project description:MicroRNAs (miRNAs) play important roles in leukocyte differentiation, although those utilised for specific programs and key functions remain incompletely characterised. We are therefore to identify a unique miRNA network that is intimately linked to the mast cell differentiation program.

2014-08-01 | E-MTAB-2443 | biostudies-arrayexpress

The homeobox transcription factor Nkx2-1 regulates microRNAs controlling downstream gene silencing in lung epithelial cells (microRNA)

Project description:Cell-specific gene expression is achieved by a combination of mechanisms including transcriptional and post-transcriptional regulation. The transcription factor Nkx2-1, essential for lung cell differentiation, mainly acts in transcriptional activation but can directly or indirectly repress gene expression. microRNAs are a class of small non-coding RNA that control one of the major mechanisms of gene repression. To identify miRNAs regulated by Nkx2-1 that may mediate its repressing effects, we knocked-down Nkx2-1 in mouse lung epithelial cell lines and systematically identified targets by genome-wide miR and mRNA expression analyses. Nkx2-1 controls expression of miRs known to contribute to lung cell differentiation in development and disease and others not previously described. Amongst the significantly altered miRs, the mir-106a-363 cluster, miR-1195, miR-378, and miR-346 are directly correlated with the levels of Nkx2-1, whereas miR-200c/b, miR-221, and miR- 222 are inversely correlated. These miRNAs are expressed in embryonic lung at day E11.5, and/or E19.5 determined by in-situ hybridization. Expression of predicted targets of mir-1195, mir-346 and miR-200c and mir-221/222 were evaluated by mRNA expression microarrays in Nkx2-1 knockdown cells identifying those anti-correlated to the corresponding miRNA expression. Genes regulated by mir-1195, Cyp2s1 and Map3k2, by mir-346, Klf6, and miR-200c, Myb, Nfib, and Six1, were validated by qRT-PCR. Inhibition of mir-1195 confirms the inverse correlation of this miRNA with its putative targets Cyp2s1 and Map3k2. This miRNA-mRNA expression analysis identifies potential paths of Nkx2-1 mediated gene repression, and contributes to the understanding of gene regulation in lung epithelial differentiation and development. Nkx2-1 mRNA was knocked down in lung epithelial cells using a lentivirus expressing a shRNA targeting Nkx2-1 (n=3) and compared to empty vector controls (n=3).

2015-12-22 | E-GEOD-47053 | biostudies-arrayexpress

MiR expression profile in M1-polarized bone marrow derived macrophage cells compared with normal mouse aortic tissue.

Project description:The global change of the miR expression profile during atherosclerosis is due to the infiltration of different types of leukocytes into the arterail vessel wall in addition to disease-specific regulation in vascular cells. Monocyte-derived macrophage accumulation in the subintimal region is critical in the formation of atherosclerotic plaques. It is currently unknown which miRs are involved in the atherogenic macrophage response. The comparison of the miR expression profile in LPS/Interferon-gamma activated mouse macrophages with the miR expression in the normal aortic vessel wall was performed to detect macrophage-enriched miRs. This screening may help to identify macrophage-enriched miRs in atherosclerotic vessels that may play a role in the macrophage function during atherogenesis. Bone marrow cells were harvested from femura of 6-8 week old female C57BL/6 mice, re-suspended in DMEM-F12/10% FCS/10% L929-conditioned medium, and cultured for 7 days to differentiate into primary macrophages. F4/80 and CD11b expression was determined by flow cytometry to confirm the macrophage phenotype. Macrophages were stimulated with LPS (100ng/ml, 14 hours) and INF-g (10ng/ml, 6 hours) and the M1 polarization was verified by quantification of mannose receptor C type 1 (MRC1), arginase II (ArgII), inducible nitric oxide synthase (iNOS), and arginase I (ArgI) by qRT-PCR. Total RNA (M1-type macrophages and aorta tissue) was isolated using mirVana microRNA Isolation Kit.

2014-01-01 | E-GEOD-26556 | biostudies-arrayexpress

miRNA expression profile of pre-transfected HEY cells

Project description:MicroRNAs (miRNAs) are short (~22 nucleotides) regulatory RNAs that can modulate gene expression and are aberrantly expressed in many diseases including cancer. We wanted to quantify the levels of endogenous miRNAs in pre-transfected HEY ovarian cancer cells to identify the highly expressed miRNAs. It was previously established that transfection of small RNAs can globally perturb gene expression, and one mechanism responsible for such alterations may involve de-repression of targets of endogenous miRNAs because of the saturation of the RISC complexes by the exogenously administered small RNA (Khan et al., 2009. Nat Biotechnol 27, 549-555). By measuring the levels of miRNAs in the pre-transfected HEY cells, we wanted to determine the miRNAs most highly expressed in HEY cells, and therefore, most likely to experience the effects of such competition. miRNAs were collected from duplicate wells of HEY cells grown in 6-well plates after ~64 hours of seeding (~1.5E5 cells/well). The miRNA expression pattern was determined using an Affymetrix GeneChip miRNA Array.

2012-04-08 | E-GEOD-29126 | 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