Similar Datasets
Project description:Plasma ceRNA expression profiles were acquired by using a human ceRNA microarray.
2020-04-14 | GSE148602 | GEO
Project description:Circulating long noncoding RNAs associated with hypertrophic cardiomyopathy
| PRJNA601680 | ENA
Project description: Not available
| S-EPMC7646839 | biostudies-literature
Project description:Approximately 1426 lncRNAs (965 up-regulated and 461 down-regulated) and 1715 mRNAs (896 up-regulated and 819 down-regulated) were aberrantly expressed in HCM patients with fold change > 2.0 Myocardial tissues were obtained from 7 HCM patients and 5 disease-free individuals, and lncRNA and mRNA expression profiles were analyzed using the CapitalBio Human LncRNA Microarray v2.0.
2015-05-08 | E-GEOD-68316 | biostudies-arrayexpress
Project description: Not available
| S-EPMC8430576 | biostudies-literature
Project description:Hypertrophic cardiomyopathy (HCM) is the most common heritable cardiomyopath that caused by mutations in genes encoding proteins of the cardiac sarcomere. Although multiple efforts have been made to understand the pathogenesis of HCM, the mechanisms of how long noncoding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) network result in HCM still unkown. Herein, we acquired the different expression profiles of lncRNAs (DElncRNAs) and messenger RNAs (mRNA, DEGs) by using microarray, microRNAs (DEmiRNAs) by sequencing in plasma of HCM patients and healthy controls. LncRNA-miRNA pairs were predicted using miRcode and starBase, and crossed with DEmiRNAs. MiRNA-mRNA pairs were retrieved from miRanda and TargetScan, and crossed with DEGs. Combined these pairs, the ceRNA network was constructed and hub nodes were then analyzed to reconstruct subnetwork. Gene Ontology and KEGG pathways were used to analyse the mRNAs in the ceRNA. Total 520 DElncRNAs, 33 DEmiRNAs, and 371 DEGs were identified. By coexpression analysis, 682 lncRNA-mRNA pairs were identified with a coefficient ≥ 0.9 and p < 0.05. The ceRNA network with 8 lncRNAs, 3 miRNAs and 22 mRNAs was constructed visualized by Cytoscape. LncRNA RP11-66N24.4 and LINC00310 are among the top 10% nodes and the associated ceRNA subnetwork may be the center of the whole ceRNA network. Furthermore, the qRT-PCR results showed that LINC00310 was signifcantly decreased in HCM patients. For LINC00310, GO analysis revealed that the biological processes was enriched in cardiovascular system development, sprouting angiogenesis, circulatory system development and so on, and Pathway analysis was mainly enriched in cGMP-PKG signaling pathway. Our study reveals the novel lncRNA-related ceRNA network in HCM and the identified lncRNA LINC00310 may be roles in the pathogenesis mechanisms of HCM, which could provide further insight into the pathogenesis of HCM.
2022-09-28 | GSE197218 | GEO
Project description:Long non-coding RNAs (lncRNAs) are generally defined as RNA transcripts longer than 200 nucleotides that are not translated into proteins. Recently, many small open reading frames (smORFs) embedded in lncRNA scripts have been verified to be able to encode functional polypeptides (namely lncRNA-SEPs here). Although collaborative analysis by advanced genomics, bioinformatics and proteomics largely drives SEPs discovery, the poor predictability, diminutive size and low abundance still challenge systematic identification of SEPs from different biological samples. Here, we took advantage of the NONCODE database that deposited with the most complete collection and annotation of lncRNA transcripts from different species to build a database that to maximally collect all putative small ORFs from human and mouse lncRNA transcripts. Two effective and complementary polypeptides enrichment strategies (30 kDa MWCO filter and C8 SPE column) were also integrated to further improve the discovery of novel lncRNA-SEPs. These efforts led to the discovery of 362 lncRNA-SEPs from 8 human cell lines and 238 lncRNA-SEPs from 3 mouse cell lines and 8 mouse tissues. 18 out of these lncRNA-SEPs were verified experimentally by multiple technologies including in vitro expression, immunoblotting and parallel reaction monitoring-based mass spectrometry (PRM-MS) in 293T cells. Further bioinformatic analysis reveals that the physical and chemical properties of these novel lncRNA-SEPs, such as amino acid composition and codon usage, are varied from canonical proteins. Intriguingly, nearly 70% of the identified lncRNA-SEPs were found to be initiated with non-AUG start codons. Collectively, the efficient workflows presented in this study enables us identify 600 novel lncRNA-SPEs from multiple cell lines and tissues, which should represent the largest number of MS-detected lncRNA-encoding SEPs ever reported to date. These novel lncRNA-SEPs not only could provide new clues for the annotation of the noncoding elements in the genome, but also could serve as a valuable resource for the functional characterization of individual lncRNA-SEPs.
2023-05-06 | PXD016981 | Pride
Project description:Hypertrophic cardiomyopathy (HCM) is the most common heritable cardiomyopath that caused by mutations in genes encoding proteins of the cardiac sarcomere. Although multiple efforts have been made to understand the pathogenesis of HCM, the mechanisms of how long noncoding RNA (lncRNA)-associated competing endogenous RNA (ceRNA) network result in HCM still unkown. Herein, we acquired the different expression profiles of lncRNAs (DElncRNAs) and messenger RNAs (mRNA, DEGs) by using microarray, microRNAs (DEmiRNAs) by sequencing in plasma of HCM patients and healthy controls. LncRNA-miRNA pairs were predicted using miRcode and starBase, and crossed with DEmiRNAs. MiRNA-mRNA pairs were retrieved from miRanda and TargetScan, and crossed with DEGs. Combined these pairs, the ceRNA network was constructed and hub nodes were then analyzed to reconstruct subnetwork. Gene Ontology and KEGG pathways were used to analyse the mRNAs in the ceRNA. Total 520 DElncRNAs, 33 DEmiRNAs, and 371 DEGs were identified. By coexpression analysis, 682 lncRNA-mRNA pairs were identified with a coefficient ≥ 0.9 and p < 0.05. The ceRNA network with 8 lncRNAs, 3 miRNAs and 22 mRNAs was constructed visualized by Cytoscape. LncRNA RP11-66N24.4 and LINC00310 are among the top 10% nodes and the associated ceRNA subnetwork may be the center of the whole ceRNA network. Furthermore, the qRT-PCR results showed that LINC00310 was signifcantly decreased in HCM patients. For LINC00310, GO analysis revealed that the biological processes was enriched in cardiovascular system development, sprouting angiogenesis, circulatory system development and so on, and Pathway analysis was mainly enriched in cGMP-PKG signaling pathway. Our study reveals the novel lncRNA-related ceRNA network in HCM and the identified lncRNA LINC00310 may be roles in the pathogenesis mechanisms of HCM, which could provide further insight into the pathogenesis of HCM.
2022-09-28 | GSE197191 | GEO
Project description:Ischemic cardiomyopathy(ICM) and dilated cardiomyopathy(DCM), with distinct long-term prognosis and responses to treatment, are two major problems that lead to heart failure(HF) ultimately. In this study, we investigated the lncRNA and mRNA expressions in the plasma of patients with DCM and ICM and analyzed the different lncRNA profile between the two groups. These findings revealed for the first time the specific expression pattern of both protein-coding RNAs and lncRNAs in plasma of HF patients due to DCM and ICM which may provide some important evidence to conveniently identify the etiology of myocardial dysfunctions and help to explore a better strategy for future HF prognosis evaluation.
2022-10-08 | GSE138678 | GEO
Project description:Noncoding RNAs include small transcripts, such as microRNAs and piwi-interacting RNAs, and a wide range of long noncoding RNAs (lncRNAs). Although many lncRNAs have been identified, only a small number of lncRNAs have been characterized functionally. Here, we sought to identify lncRNAs differentially expressed during replicative senescence. We compared lncRNAs expressed in proliferating, early-passage, 'young' human diploid WI-38 fibroblasts [population doubling (PDL) 20] with those expressed in senescent, late-passage, 'old' fibroblasts (PDL 52) by RNA sequencing (RNA-Seq). Numerous transcripts in all lncRNA groups (antisense lncRNAs, pseudogene-encoded lncRNAs, previously described lncRNAs and novel lncRNAs) were validated using reverse transcription (RT) and real-time, quantitative (q)PCR. Among the novel senescence-associated lncRNAs (SAL-RNAs) showing lower abundance in senescent cells, SAL-RNA1 (XLOC_023166) was found to delay senescence, because reducing SAL-RNA1 levels enhanced the appearance of phenotypic traits of senescence, including an enlarged morphology, positive β-galactosidase activity, and heightened p53 levels. Our results reveal that the expression of known and novel lncRNAs changes with senescence and suggests that SAL-RNAs play direct regulatory roles in this important cellular process. RNA was extracted from both young and senescent WI-38 cells and used for total RNA-Seq.
2016-02-08 | E-GEOD-77675 | biostudies-arrayexpress