Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

51 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mouse embryo or newborn liver or E15.5 embryo minus liver vs. pool of all samples

ABSTRACT: Transcriptional profiling of miRNA in embryonic and newborn mouse liver Keywords: miRNA, liver, newborn, embryonic Time course experiment with common control. Three biological replicates per time point.

ORGANISM(S): Mus musculus

SUBMITTER: Joshua Friedman

PROVIDER: E-GEOD-10602 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

The microRNA-30 family is required for vertebrate hepatobiliary development.

Hand Nicholas J NJ Master Zankhana R ZR Eauclaire Steven F SF Weinblatt Daniel E DE Matthews Randolph P RP Friedman Joshua R JR

Gastroenterology 20081209 3

<h4>Background & aims</h4>The function of microRNA (miRNA) in liver development is unknown. To address this issue, we characterized miRNA expression in the embryonic mouse liver, performed functional miRNA analysis in zebrafish larvae, and identified novel hepatic miRNA targets.<h4>Methods</h4>Hepatic RNA isolated from mice at embryonic days 15.5, 18.5, and postnatal day 2 was hybridized to a mouse miRNA microarray. The microarray results were confirmed by Northern blot hybridization and quantit ...[more]

PMID: 19185580

Similar Datasets

Mature thymic NKT and T cells

Project description:Invariant Natural killer T (iNKT) cells are a separate lineage of T lymphocytes with innate effector functions. They express an invariant TCR specific for lipids presented by CD1d and their development and effector differentiation rely on a unique gene expression program. We asked whether this program includes microRNAs, small non-coding RNAs that regulate gene expression posttranscriptionally and play key role in the control of cellular differentiation programs. We identified a miRNA profile specific for iNKT cells, which exhibits features of activated/effector T lymphocytes. In this experiment we compared microRNAs of NKT cells versus those of conventional T lymphocytes, both extracted from wild type mouse thymus. To produce the populations we enriched mature thymocytes and then sorted NKT cells and conventional T cells (from one sorting we obtain one â??NKTâ?? sample and one â??Tâ?? sample). We performed the experiment in triplicate; the sample NKT 1 was sorted the same day of the sample T 1, NKT 2 with T 2, NKT 3 with T 3. We used a common reference approach for the 6 samples; as a common reference we produced RNA from total thymocytes, without the enrichment for mature cells and without the sorting; we pooled thymocytes derived from all the thymi used in the study. The aim of the experiment was to demonstrate that NKT cells have a microRNA profile different from that of conventional T cells.

2010-04-09 | E-GEOD-15925 | biostudies-arrayexpress

Differential regulation of microRNA in ocular wound healing

Project description:Pterygium is a relatively common human ocular surface fibroproliferative disease that affects vision. Endogenously produced microRNA (miRNA) regulates gene expression in various ocular surface diseases and possibly pterygium. We aimed to investigate the role of miRNA in pterygium. Paired human pterygium and conjunctival tissues were obtained from patients diagnosed with primary pterygium. miRNA microarray profiling identified statistically significant miRNA changes which were matched to reciprocal significant changes in their target transcripts. We employed quantitative real-time polymerase chain reaction and found that hsa-miR-766 was up-regulated (2.57-fold) whilst hsa-miR-215 was down-regulated (0.49-fold) in pterygium compared to conjunctival control. Localization of miRNA was performed using in-situ hybridization. Transcript levels of predicted hsa-miR-766 targets, nuclear receptor subfamily 4, group A, member 1 and epidermal growth factor-containing fibulin-like extracellular matrix protein 1, were down-regulated in pterygium compared to conjunctiva by 0.53- and 0.64-fold, respectively. Collagens type 3, alpha 1 and type 4, alpha 2, both targets of hsa-miR-215, were up-regulated in pterygium by 3.01- and 3.11-fold, respectively. These changes were confirmed in the protein levels using immunofluorescent staining. Derangement of hsa-miR-766 and hsa-miR-215 may cause dysregulation of matrix rearrangement, cell proliferation and adhesion proteins, resulting in pterygium formation. Targeting miRNA may be a possible therapeutic approach in this disease. 3 pterygium samples and 3 matched conjuctiva samples from patients diagnosed with primary pterygium. A pool of all 6 samples was used as the common reference.

2010-04-28 | E-GEOD-21346 | biostudies-arrayexpress

Stimulation of human umbilical venous endothelial cells (HUVECs) with bone morphogenetic protein 4 (BMP4).

Project description:Backround: Several microRNAs have been characterized to regulate the process of angiogenesis. Previously, bone morphogenetic protein 4 (BMP4) was shown to increase the proangiogenic activity of endothelial cells. Aim: In this project we investigated how the proangiogenic BMP4 effect is mediated by microRNAs. Experimental design: To investigate changes in the microRNA transcriptome in HUVECs a time course experiment (12, 18 and 24 h) was performed. HUVECs were kept in endothelial basal medium either with BMP4 (25 ng/ml) stimulation or buffer control (4 mM HCL with 0.1% bovine serum albumin). Comparison between stimulated vs. unstimulated cells at different time points. followed by a miRNA microarray analysis was performed.

2017-02-01 | E-MTAB-4383 | biostudies-arrayexpress

Control of oligodendroglial cell number by the miR-17~92 family of miRNA cluster (miRNA Exiqon Part)

Project description:The generation of myelinating cells in the central nervous system (CNS) requires the initiation of specific gene-expression programs in oligodendrocytes. We reasoned that miRNAs could play an important role in this process by regulating critical developmental genes. Microarray profiling of cultured oligodendrocytes identifies the miR-17~92 family of miRNA cluster as highly enriched miRNAs in oligodendrocytes.We specifically deleted the miR-17~92 cluster in oligodendrocytes using the 2Â´3Â´-cyclic nucleotide 3Â´-phosphodiesterase (CNP)-Cre mice. Absence of miR-17~92 leads to a reduction of oligodendrocyte number in vivo and we find that the expression of these miRNAs in primary cultures of oligodendrocytes promotes cell proliferation by influencing Akt signalling. Together, these results suggest that the miRNA pathway is essential in determining oligodendroglial cell number and that the miR-17~92 cluster is crucial in this process. miRNA microarray profiling was used for the identification of miRNAs enriched in oligodendrocytes. Total RNA lysates from primary oligodendroctes compared to primary astrocytes were analysed regarding their miRNA levels. Three independent samples for each of the two cell types were used. The study was initially designed with a comparison of oligodendrocytes, astrocytes and microglia. However, only the comparison of oligodendrocytes and astrocytes is discussed in the present study.

2010-06-08 | E-GEOD-21799 | biostudies-arrayexpress

Mouse embryo or newborn liver or E15.5 embryo minus liver vs. pool of all samples

Project description:Transcriptional profiling of miRNA in embryonic and newborn mouse liver Keywords: miRNA, liver, newborn, embryonic

2008-02-23 | GSE10602 | GEO

Performance Evaluation of Commercial miRNA Expression Array Platforms

Project description:This data is part of a miRNA platform comparison study. We compared the performance characteristics of four commercial miRNA array technologies and found that all platforms performed well in separate measures of performance. The Ambion and Agilent platforms were more accurate, whereas the Illumina and Exiqon platforms were more specific. Furthermore, the data analysis approach had a large impact on the performance, predominantly by improving precision. Performance of four (4) commercially available miRNA platforms was evaluated using 7 placenta samples spiked with synthetic microRNA spikes (in Latin-square design) absent in placenta. Platforms were primarily evaluated for accuracy and specificity.

2010-06-23 | E-GEOD-19248 | biostudies-arrayexpress

MicroRNA-674-5p/5-LO axis is important in concanavalin A-induced acute mouse liver injury

Project description:Eight-week-old male pathogen-free BALB/c mice were used for the induction of concanavalin A (Con A)-induced hepatitis. Animals were acclimated for at least 6-7 days to a 12-hour light/dark cycle in a humidity- and temperature-controlled, specific-pathogen-free environment in autoclaved cages. Mice were randomly assigned to two groups (4 in each group) and received Con A type IV (or saline) intravenously via the tail vein at the dose of 20 mg/kg for 2 hours. The animals were sacrificed for blood and liver collection. Blood was taken for transaminase and cytokine measurements. Livers were excised immediately after sacrifice. Part of the livers were immediately snap-frozen in liquid nitrogen and kept at -80Â°C for total RNA isolation and microRNA microarray analysis. miR-674-5p and other miRNAs were experimentally validated to be dysregulated by Con A in mouse livers. Liver samples from four mice treated with Con A and four mice treated with saline were used to acquire the miRNA expression profiling.

2016-06-27 | E-GEOD-76345 | biostudies-arrayexpress

Diesel exhaust particle (DEP)-treated HBE cells

Project description:We evaluated the profile of lncRNA and mRNA expression in control and 50Î¼g/ml DEP treated HBE cells using the Arraystar Human LncRNA Array v3.0 array,7th generation. Our findings implicates that dysregulation of mitochondria invovled mRNAs may play important role in cytotoxicity of DEP. Examination of lncRNA and mRNA expression in control or DEP-treated HBE cells

2016-06-30 | E-GEOD-82335 | biostudies-arrayexpress

microRNA profiles of nasopharyngeal carcinoma cell line and nasopharyngeal epithelial cell line

Project description:Exosomal and cellular miRNA expression levels were measured using a microRNA chip array or quantitative reverse transcription PCR (qRT-PCR). miR-24-3p was enriched in T-EXOs from the sera of NPC patients and NPC cells, which was correlated with worse disease-free survival (DFS). Exosomes (miR-24-3p-sponge-EXO) released from miR-24-3p-sponge-TW03 cells failed to inhibit T-cell proliferation and Th1 and Th17 differentiation or to induce Treg differentiation in vitro, compared with controlNC -sponge-EXO. Mechanistic analyses revealed that in miR-24-3p-sponge-EXO-treated T-cells, P-ERK, P-STAT1 and P-STAT3 were up-regulated, whereas P-STAT5 was down-regulated compared with controlNC-sponge-EXO-treated T-cells. FGF11 was identified as a direct target gene of miR-24-3p through in vivo and in vitro assessments. More importantly, the T-EXOs repressed FGF11 expression in T-cells during proliferation and differentiation. Interestingly, when FGF11 expression in T-cells was blocked, miR-24-3p-sponge-EXOs impeded shFGF11-T-cell proliferation and Th1 and Th17 differentiation but induced Treg differentiation, like controlNC-sponge-EXO. When FGF11 was knocked down in miR-24-3p-sponge-EXO-treated T-cells, neither P-ERK, P-STAT1 and P-STAT3 up-regulation or P-STAT5 down-regulation occurred. Interestingly, FGF11 expression in tumor-infiltrating lymphocytes (TILs) was significantly and positively correlated with the number of CD4+ and CD8+ TILs and predicted favorable DFS of the patients (p < 0.05). Two-condition experiment, one nasopharyngeal carcinoma cell line TW03 vs. one normal epithelium cell line NP69. Biological replicates: 1 nasopharyngeal carcinoma cell line TW03; 1 nasopharyngeal epithelial cell line NP69.

2016-08-01 | E-GEOD-76527 | biostudies-arrayexpress

miRNA expression profile in intestinal ischemia reperfusion of adult mice

Project description:Intestinal ischemia/reperfusion (I/R) contributes to tissue damage, cellular apoptosis, systemic inflammatory responses, and even multiple organ dysfunction syndrome, however, underlying mechanisms remain unkown. In this report, we provide a comprehensive assessment of the expression of 1177 miRNAs on intestine tissues from mice suffering from sham and intestinal I/R. We find that 57 miRNA are up-regulated and 74 are down-regulated significantly. MiRNAs may be integral modulators of intestinal inflammation and enterocyte apoptosis associated with I/R and represent novel targets for future therapeutics. In the study, we profiled miRNA expression in the intestine from mice of 3 sham group and 3 intestinal ischemia/reperfusion group.

2016-06-25 | E-GEOD-83701 | 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