Analysis of microRNA Microarrays in Cardiogenesis

2015 ◽  
pp. 207-221 ◽  
Author(s):  
Diego Franco ◽  
Fernando Bonet ◽  
Francisco Hernandez-Torres ◽  
Estefania Lozano-Velasco ◽  
Francisco J. Esteban ◽  
...  
Keyword(s):  
Microrna Microarrays

scholarly journals Exploring the Mechanism of Baicalin Intervention in Breast Cancer Based on MicroRNA Microarrays and Bioinformatics Strategies

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
Anqi Ge ◽  
Lifang Liu ◽  
Xian’guang Deng ◽  
Jun Luo ◽  
Yanghua Xu
Keyword(s):  
Breast Cancer ◽  
Cancer Cells ◽  
Signaling Pathway ◽  
Breast Cancer Cells ◽  
Enrichment Analysis ◽  
Dependent Manner ◽  
P53 Signaling ◽  
Microrna Microarrays ◽  
P53 Signaling Pathway ◽  
Mcf 7

Objective. To explore the mechanism of baicalin intervention in breast cancer based on microRNA microarrays. Methods. The inhibitory rate of baicalin intervention in MCF-7 breast cancer cells was determined by MTT. Then, the miRNA microarrays were used to validate the key microRNAs. After that, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to validate microRNA, hsa-miR-15a, hsa-miR-100, hsa-miR-16, and hsa-miR-7t. Finally, the potential targets of these key microRNAs are predicted by miRWalk, and DAVID was utilized for gene ontology (GO) enrichment analysis and pathway enrichment analysis. Results. Baicalin may inhibit the proliferation of MCF-7 cells in a dose-dependent and time-dependent manner. The concentration of baicalin 150 μmol/L was determined for the subsequent miRNA chip research. A total of 92 upregulated microRNAs and 35 downregulated microRNAs were obtained. The upregulated miRNAs include hsa-miR-6799-5p, hsa-miR-6126, hsa-miR-4792, hsa-miR-6848-5p, hsa-miR-3197, hsa-miR-6779-5p, and hsa-miR -654-5p. The downregulated miRNAs include hsa-miR-3911, hsa-miR-504-5p, hsa-miR-30a-3p, hsa-miR-193b-3p, and hsa-miR-181b-5p. Then, differentially expressed miRNA was verified by qRT-PCR. The results showed that the expression of hsa-miR-15a, hsa-miR-100, hsa-miR-16, and hsa-let-7c was upregulated ( P < 0.05 ), which was consistent with the results of the miRNA microarray. The enrichment analysis showed that baicalin might regulate the DNA-templated proliferation, DNA-templated transcription, p53 signaling pathway, etc., of MCF-7 breast cancer cells through miRNA. Conclusion. Baicalin inhibits the proliferation of breast cancer cells. It may achieve antitumor effects through regulating microRNAs so as to affect the DNA replication (such as cellular response to DNA damage stimulus and DNA binding), RNA transcription (such as regulation of transcription, DNA-templated, transcription from RNA polymerase II promoter, and transcription factor binding), protein synthesis (such as mRNA binding, Golgi apparatus, and protein complex), endocytosis, pathways in cancer, p53 signaling pathway, and so on.

scholarly journals Phenotypic MicroRNA Microarrays

Microarrays ◽  
2013 ◽  
Vol 2 (2) ◽  
pp. 63-80 ◽  
Author(s):  
Yong-Jun Kwon ◽  
Jin Heo ◽  
Hi Kim ◽  
Jin Kim ◽  
Michel Liuzzi ◽  
...  
Keyword(s):  
Microrna Microarrays

Simple purification of small RNAs from seeds and efficient detection of multiple microRNAs expressed in Arabidopsis thaliana and tomato (Lycopersicon esculentum) seeds

2005 ◽  
Vol 15 (4) ◽  
pp. 319-328 ◽  
Author(s):  
Ruth C. Martin ◽  
Po-Pu Liu ◽  
Hiroyuki Nonogaki
Keyword(s):  
Molecular Weight ◽  
Arabidopsis Thaliana ◽  
Lycopersicon Esculentum ◽  
Small Rnas ◽  
Detection Sensitivity ◽  
Specific Expression ◽  
Simple Method ◽  
Dna Oligomers ◽  
Efficient Detection ◽  
Microrna Microarrays

MicroRNAs (miRNAs) play critical roles in the development of animals and plants. Characterizing the stage- and tissue-specific expression of miRNAs that potentially regulate target transcription factor expression is becoming more important for understanding the regulatory mechanisms of critical events during plant development. A simple method for purifying small RNAs from seeds is described, as well as an efficient non-radioactive labelling system for making miRNA probes. In Arabidopsis thaliana seed extracts, low molecular-weight (LMW) RNAs (e.g. 5S rRNA, tRNA and miRNA) were separated from high molecular-weight (HMW) nucleic acids (e.g. 28S and 18S rRNA, mRNA and genomic DNA) by fractionation using isopropanol. HMW RNAs precipitated in 20% isopropanol, while most LMW RNAs remained in the supernatant. The purified LMW RNAs were used successfully for RNA gel blotting to detect miRNAs expressed in Arabidopsis and tomato (Lycopersicon esculentum) seeds. To increase the detection sensitivity of the microRNA probes, additional digoxigenin-labelled uridine triphosphates (UTPs) were incorporated into the miRNA probes by designing template oligo DNAs with three extra adenines (A) at each end of their sequence. These DNA oligomers were used to make double-stranded DNA templates for miRNA probe synthesis. This probe (termed AAAPLUS) exhibited stronger signals than normal probes. A technique was also developed to quickly screen expressed miRNAs in seeds using a miniblot system, which enabled simultaneous examination with multiple miRNA probes. This method provides a simple alternative to microRNA microarrays to identify the major miRNAs expressed in seeds.

scholarly journals Evaluation of normalization methods for two-channel microRNA microarrays

2010 ◽  
Vol 8 (1) ◽  
pp. 69 ◽  
Author(s):  
Yingdong Zhao ◽  
Ena Wang ◽  
Hui Liu ◽  
Melissa Rotunno ◽  
Jill Koshiol ◽  
...  
Keyword(s):  
Normalization Methods ◽  
Microrna Microarrays

scholarly journals Involvement of human monogenic cardiomyopathy genes in experimental polygenic cardiac hypertrophy

2018 ◽  
Vol 50 (9) ◽  
pp. 680-687
Author(s):  
P. R. Prestes ◽  
F. Z. Marques ◽  
G. Lopez-Campos ◽  
P. Lewandowski ◽  
L. M. D. Delbridge ◽  
...  
Keyword(s):  
Cardiac Hypertrophy ◽  
Differentially Expressed ◽  
Idiopathic Dilated Cardiomyopathy ◽  
Whole Genome ◽  
Noncoding Regions ◽  
Idiopathic Cardiomyopathy ◽  
Genes Encoding ◽  
Increasing Risk ◽  
Microrna Microarrays

Hypertrophic cardiomyopathy thickens heart muscles, reducing functionality and increasing risk of cardiac disease and morbidity. Genetic factors are involved, but their contribution is poorly understood. We used the hypertrophic heart rat (HHR), a unique normotensive polygenic model of cardiac hypertrophy and heart failure, to investigate the role of genes associated with monogenic human cardiomyopathy. We selected 42 genes involved in monogenic human cardiomyopathies to study: 1) DNA variants, by sequencing the whole genome of 13-wk-old HHR and age-matched normal heart rat (NHR), its genetic control strain; 2) mRNA expression, by targeted RNA-sequencing in left ventricles of HHR and NHR at 5 ages (2 days old and 4, 13, 33, and 50 wk old) compared with human idiopathic dilated cardiomyopathy data; and 3) microRNA expression, with rat microRNA microarrays in left ventricles of 2-day-old HHR and age-matched NHR. We also investigated experimentally validated microRNA-mRNA interactions. Whole-genome sequencing revealed unique variants mostly located in noncoding regions of HHR and NHR. We found 29 genes differentially expressed in at least 1 age. Genes encoding desmoglein 2 ( Dsg2) and transthyretin ( Ttr) were significantly differentially expressed at all ages in the HHR, but only Ttr was also differentially expressed in human idiopathic cardiomyopathy. Lastly, only two microRNAs differentially expressed in the HHR were present in our comparison of validated microRNA-mRNA interactions. These two microRNAs interact with five of the genes studied. Our study shows that genes involved in monogenic forms of human cardiomyopathies may also influence polygenic forms of the disease.

scholarly journals Stripping custom microRNA microarrays and the lessons learned about probe–slide interactions

2009 ◽  
Vol 386 (2) ◽  
pp. 222-227 ◽  
Author(s):  
Xiaoxiao Zhang ◽  
Wayne Xu ◽  
Jiankang Tan ◽  
Yan Zeng
Keyword(s):  
Lessons Learned ◽  
Microrna Microarrays

Retrieving relevant experiments: The case of microRNA microarrays

Biosystems ◽  
2015 ◽  
Vol 134 ◽  
pp. 71-78 ◽  
Author(s):  
Koray Açıcı ◽  
Yunus Kasım Terzi ◽  
Hasan Oğul
Keyword(s):  
Microrna Microarrays

scholarly journals Comparative Analyses of MicroRNA Microarrays during Cardiogenesis: Functional Perspectives

Microarrays ◽  
2013 ◽  
Vol 2 (2) ◽  
pp. 81-96 ◽  
Author(s):  
Fernando Bonet ◽  
Francisco Hernandez-Torres ◽  
Franciso Esteban ◽  
Amelia Aranega ◽  
Diego Franco
Keyword(s):  
Comparative Analyses ◽  
Microrna Microarrays

MicroRNA microarrays on archive bone marrow core biopsies of leukemias—Method validation

2011 ◽  
Vol 35 (2) ◽  
pp. 188-195 ◽  
Author(s):  
Ioana Borze ◽  
Mohamed Guled ◽  
Suad Musse ◽  
Anna Raunio ◽  
Erkki Elonen ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Method Validation ◽  
Microrna Microarrays
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