Similar Datasets
Project description:Recently, it has been demonstrated that genomes of many species express single stranded RNAs with covalently closed ends, named circular RNAs. Their regulatory potential and functional relevance are just starting to be revealed. Here we present a novel computational tool, seekCRIT (seek for differentially expressed Circular RNAs In Transcriptome), that identifies circular RNAs and detects their differential expression between two conditions. Using seekCRIT we identified the circular RNAs that are expressed in the neural retina and determined that the majority of them (74%) are expressed in both, ischemic and normal conditions. We identified over 40 circular RNAs that were differentially expressed between both conditions and validated these experimentally using qRT-PCR. The high validation rate of 90% with a false discovery rate (FDR) of < 5% demonstrates the accuracy and reliability of seekCRIT.
2021-02-02 | GSE114896 | GEO
Project description:Using microRNA-Seq, we examined the alteration of microRNA expression profiles in the nucleus accumbens of methamphetamine-sensitized and saline-control mice. Nucleus accumbens lysate from eight mice of each group were pooled as one sample. Two RNA samples from each group were prepared and were then processed to generate small RNA libraries, which were sequenced on the Illumina Hiseq 2000. The aberrant expression of microRNAs identified in this study may involve in METH-induced locomotor sensitization and addiction.
2022-07-13 | E-MTAB-2901 | biostudies-arrayexpress
Project description:The aim of this study was to identify and quantify microRNAs and other small regulatory RNAs expressed in primary retinal microvascular endothelial cells (RMECs) using deep sequencing. RMECs were isolated, RNA extracted, a small RNA library prepared and deep sequencing performed. A total of 6.8 million reads were mapped to 250 known microRNAs in miRBase (release 16). Several novel microRNAs and multiple new members of the miR-2284/2285 family were detected. Several ~30 nucleotide sno-miRNAs were identified, with the most highly expressed being derived from snoRNA U78. Highly expressed microRNAs previously associated with endothelial cells included miR-126 and miR-378, but the most highly expressed was miR-21, comprising more than one third of all mapped reads. The independence from prior sequence knowledge provided by deep sequencing facilitates analysis of novel microRNAs and other small RNAs. This approach also enables quantitative evaluation of microRNA expression, which has highlighted the predominance of a small number of microRNAs in RMECs. Further characterisation of the functions of the highly expressed microRNAs will provide insights into endothelial biology. Single sample of primary cell culture
2012-02-13 | E-GEOD-31340 | biostudies-arrayexpress
Project description:The wide application of pig disease model has caused a surge of interest in the study of derivation of pig induced pluripotent cells (iPSCs). Here we performed genome-wide analysis of gene expression profiling by RNA-seq and small RNA-seq and DNA methylation profile by MeDIP-seq in pig iPSCs through comparison with somatic cells. We identified mRNA and microRNA transcripts that were specifically expressed in pig iPSCs. Our analysis identifies the genes up-regulated in pig iPS compared with somatic cells and also the differentially expressed genes between pig iPSCs under different culture medium. We then pursued comprehensive bioinformatics analyses, including functional annotation of the generated data within the context of biological pathways, to uncover novel biological functions associated with maintenance of pluripotency in pig. This result supports that pig iPS have transcript profiles linked to “ribosome”, “chromatin remodeling”, and genes involved in “cell cycle “that may be critical to maintain their pluripotency, plasticity, and stem cell function. Our analysis demonstrates the key role of RNA splicing in regulating the pluripotency phenotype of pig cells. Specifically, the data indicate distinctive expression patterns for SALL4 spliced variants in different pig cell types and highlight the necessity of defining the type of SALL4 when addressing the expression of this gene in pig cells. MeDIP-seq data revealed that the distribution patterns of methylation signals in pig iPS and somatic cells along the genome. We identify 25 novel porcine miRNA, including pluripotency-related miR-302/367cluster up-regulated in pig iPSCs. At last, we profile the dynamic gene expression signature of pluripotent genes in the preimplantation development embryo of pig. The resulting comprehensive data allowed us to compare various different subsets of pig pluripotent cell. This information provided by our analysis will ultimately advance the efforts at generating stable naïve pluripotency in pig cells.
2015-05-08 | E-MTAB-2631 | biostudies-arrayexpress
Project description:The wide application of pig disease model has caused a surge of interest in the study ofderivation of pig induced pluripotent cells (iPSCs). Here we performed genome-wide analysis of gene expression profiling by RNA-seq and small RNA-seq and DNA methylation profile by MeDIP-seq in pig iPSCs through comparison with somatic cells. We identified mRNA and microRNA transcripts that were specifically expressed in pig iPSCs. Our analysis identifies the genes up-regulated in pig iPS compared with somatic cells and also the differentially expressed genes between pig iPSCs under different culture medium. We then pursued comprehensive bioinformatics analyses, including functional annotation of the generated data within the context of biological pathways, to uncover novel biological functions associated with maintenance of pluripotency in pig. This result supports that pig iPS have transcript profiles linked to M-bM-^@M-^\ribosomeM-bM-^@M-^], M-bM-^@M-^\chromatin remodelingM-bM-^@M-^], and genes involved in M-bM-^@M-^\cell cycle M-bM-^@M-^\that may be critical to maintain their pluripotency, plasticity, and stem cell function. Our analysis demonstrates the key role of RNA splicing in regulating the pluripotency phenotype of pig cells. Specifically, the data indicate distinctive expression patterns for SALL4 spliced variants in different pig cell types and highlight the necessity of defining the type of SALL4 when addressing the expression of this gene in pig cells. MeDIP-seq data revealed that the distribution patterns of methylation signals in pig iPS and somatic cells along the genome. We identify 25 novel porcine miRNA, including pluripotency-related miR-302/367cluster up-regulated in pig iPSCs. At last, we profile the dynamic gene expression signature of pluripotent genes in the preimplantation development embryo of pig. The resulting comprehensive data allowed us to compare various different subsets of pig pluripotent cell. This information provided by our analysis will ultimately advance the efforts at generating stable naM-CM-/ve pluripotency in pig cells.
2015-09-17 | E-MTAB-2634 | biostudies-arrayexpress
Project description:Allopolyploidy is long recognized as an essential driving force in plant evolution. Recent studies have demonstrated that small RNAs, including microRNAs (miRNAs), play important roles in the process of allopolyploidy. However, the question that how the distinct parent-of-origin miRNAs are maintained in allopolyploids and how these small RNAs affect gene expression and phenotypes remain to be answered. Therefore, we investigated the miRNA expression profiles of a synthesized allotetraploid, Cucumis ×hytivus and its parents. The different developmental stages of leaves of C. ×hytivus showing contrasting leaf colour were compared as well. Following high-throughput sequencing, 546 conserved and 287 novel miRNAs were identified. The expression levels of nine miRNAs obtained by quantitative real-time PCR were consistent with the sequencing results. We detected that 15 miRNAs were divergently expressed between the parent species, and 23 miRNAs were differentially expressed in C. ×hytivus compared to either of its parents or both, which suggests the significant effect of allopolyploidization on miRNAs accumulation. Additionally, 26 conserved and 13 novel miRNAs differed in expression between the young and mature leaves of C. ×hytivus, indicating an essential role of miRNA-mediated regulation of leaf development following allopolyploidization. This study enriches the context of allopolyploidy effect on miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in phenotypic variation in allopolyploids.
2019-08-25 | GSE79757 | GEO
Project description:The aim of this study was to identify and quantify microRNAs and other small regulatory RNAs expressed in primary retinal microvascular endothelial cells (RMECs) using deep sequencing. RMECs were isolated, RNA extracted, a small RNA library prepared and deep sequencing performed. A total of 6.8 million reads were mapped to 250 known microRNAs in miRBase (release 16). Several novel microRNAs and multiple new members of the miR-2284/2285 family were detected. Several ~30 nucleotide sno-miRNAs were identified, with the most highly expressed being derived from snoRNA U78. Highly expressed microRNAs previously associated with endothelial cells included miR-126 and miR-378, but the most highly expressed was miR-21, comprising more than one third of all mapped reads. The independence from prior sequence knowledge provided by deep sequencing facilitates analysis of novel microRNAs and other small RNAs. This approach also enables quantitative evaluation of microRNA expression, which has highlighted the predominance of a small number of microRNAs in RMECs. Further characterisation of the functions of the highly expressed microRNAs will provide insights into endothelial biology.
2012-02-13 | GSE31340 | GEO
Project description:Smoking is a significant risk factor for lung cancer, the leading cause of cancer-related deaths worldwide. While microRNAs are regulators of many airway gene-expression changes induced by smoking, their role in modulating changes associated with lung cancer in these cells remains unknown. Here, we use next-generation sequencing of small RNAs in the airway to identify miR-4423 as a novel primate-specific microRNA associated with lung cancer and expressed primarily in mucociliary epithelium. The endogenous expression of miR-4423 increases as bronchial epithelial cells undergo differentiation into mucociliary epithelium in vitro and its overexpression during this process causes an increase in the number of ciliated cells. Furthermore, expression of miR-4423 is reduced in most lung tumors and in cytologically normal epithelium of the mainstem bronchus of smokers with lung cancer. In addition, ectopic expression of miR-4423 in a subset of lung cancer cell lines reduces their anchorage-independent growth and significantly decreases the size of the tumors formed in a mouse xenograft model. Consistent with these phenotypes, overexpression of miR-4423 induces a differentiated-like pattern of airway epithelium gene expression and reverses the expression of many genes that are altered in lung cancer. Together, our results indicate that miR-4423 is a novel regulator of airway epithelium differentiation and that the abrogation of its function contributes to lung carcinogenesis. Small RNA expression was profiled from pooled bronchial airway epithelial cell brushings (n=3 patients/pool) obtained during bronchoscopy from healthy never (NS) and current smokers (S) and smokers with (C) and without (NC) lung cancer. MicroRNA hsa-miR-4423 was over expressed in H1299, Calu6, SW900 and H2170 lung cancer cell lines.
2013-10-08 | E-GEOD-32726 | biostudies-arrayexpress
Project description: Not available
| S-EPMC2896132 | biostudies-literature
Project description: Not available
| S-EPMC2767369 | biostudies-literature