Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Integrated analysis of long noncoding RNAs and mRNA expression profiles reveals the potential role of lncRNAs in early stage of post-peripheral nerve injury in Sprague-Dawley rats.

ABSTRACT: The regulatory role of lncRNAs in the early stage post peripheral nerve injury (PNI) is not yet clear. In this study, next-generation sequencing was used to perform deep sequencing on normal sciatic nerves (control) and lesional tissues derived on the 4th (D4) and 7th days (D7) after sciatic nerve injury in rats. Time-point unique differentially expressed lncRNAs (DElncRNAs) were analyzed for functional enrichment. The results showed that 776 DElncRNAs were unique to D4, and their functions were mainly enriched in wound healing, phosphatase binding and MAPK signaling pathways; 317 DElncRNAs were unique to D7, and their functions were mainly enriched in ion transmembrane transporter channel activity; 579 DElncRNAs were shared by these two days, and their functions were mainly enriched in axongenesis, the PI3K-Akt signaling pathway and cell cycle. Furthermore, lncRNA-mRNA interaction networks were constructed in functions or pathways with a high enrichment rate. Finally, 3 mRNAs and 4 lncRNAs in the axongenesis interaction network were selected, and their expression levels were verified by RT-qPCR. This study preliminarily revealed the regulatory role of lncRNAs at different time points in the early stage post PNI, which provides potential targets for basic research and clinical treatment of PNI.

SUBMITTER: Zhang Y

PROVIDER: S-EPMC8202893 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Integrated analysis of long noncoding RNAs and mRNA expression profiles reveals the potential role of lncRNAs in early stage of post-peripheral nerve injury in Sprague-Dawley rats

Project description:The regulatory role of lncRNAs in the early stage post peripheral nerve injury (PNI) is not yet clear. In this study, next-generation sequencing was used to perform deep sequencing on normal sciatic nerves (control) and lesional tissues derived on the 4th (D4) and 7th days (D7) after sciatic nerve injury in rats. Time-point unique differentially expressed lncRNAs (DElncRNAs) were analyzed for functional enrichment. The results showed that 776 DElncRNAs were unique to D4, and their functions were mainly enriched in wound healing, phosphatase binding and MAPK signaling pathways; 317 DElncRNAs were unique to D7, and their functions were mainly enriched in ion transmembrane transporter channel activity; 579 DElncRNAs were shared by these two days, and their functions were mainly enriched in axongenesis, the PI3K-Akt signaling pathway and cell cycle. Furthermore, lncRNA-mRNA interaction networks were constructed in functions or pathways with a high enrichment rate. Finally, 3 mRNAs and 4 lncRNAs in the axongenesis interaction network were selected, and their expression levels were verified by RT-qPCR. This study preliminarily revealed the regulatory role of lncRNAs at different time points in the early stage post PNI, which provides potential targets for basic research and clinical treatment of PNI.

2021-04-30 | GSE162548 | GEO

Expression Profiles of Long Noncoding RNAs and Messenger RNAs in Mn-Exposed Hippocampal Neurons of Sprague-Dawley Rats Ascertained by Microarray: Implications for Mn-Induced Neurotoxicity.

Project description:Manganese (Mn) is an essential trace element, while excessive expose may induce neurotoxicity. Recently, lncRNAs have been extensively studied and it has been confirmed that lncRNAs participate in neural functions and aberrantly expressed lncRNAs are involved in neurological diseases. However, the pathological effects of lncRNAs on Mn-induced neurotoxicity remain unclear. In this study, the expression profiles of lncRNAs and messenger RNAs (mRNAs) were identified in Mn-treated hippocampal neurons and control neurons via microarray. Bioinformatic methods and intersection analysis were also employed. Results indicated that 566, 1161, and 1474 lncRNAs meanwhile 1848, 3228, and 4022 mRNAs were aberrantly expressed in low, intermediate, and high Mn-exposed groups compared with the control group, respectively. Go analysis determined that differentially expressed mRNAs were targeted to biological processes, cellular components, and molecular functions. Pathway analysis indicated that these mRNAs were enriched in insulin secretion, cell cycle, and DNA replication. Intersection analysis denominated that 135 lncRNAs and 373 mRNAs were consistently up-regulated while 150 lncRNAs and 560 mRNAs were consistently down-regulated. Meanwhile, lncRNA BC079195 was significantly up-regulated while lncRNAs uc.229- and BC089928 were significantly down-regulated in three comparison groups. The relative expression levels of 3 lncRNAs and 4 mRNAs were validated through qRT-PCR. To the best of our knowledge, this study is the first to identify the expression patterns of lncRNAs and mRNAs in hippocampal neurons of Sprague-Dawley rats. The results may provide evidence on underlying mechanisms of Mn-induced neurotoxicity, and aberrantly expressed lncRNAs/mRNAs may be useful in further investigations to detect early symptoms of Mn-induced neuropsychiatric disorders in the central nervous system.

| S-EPMC4706437 | biostudies-literature

Integrated analysis of long noncoding RNAs and mRNA expression profiles reveals the potential role of lncRNAs in early stage of post-peripheral nerve injury in Sprague-Dawley rats

Project description:Integrated analysis of long noncoding RNAs and mRNA expression profiles reveals the potential role of lncRNAs in early stage of post-peripheral nerve injury in Sprague-Dawley rats

| PRJNA682190 | ENA

Solexa sequencing of small RNAs in Sprague-Dawley (SD) rat [proximal sciatic nerve]

Project description:We applied Solexa sequencing technology to identify rat microRNA genes in proximal sciatic nerve following sciatic nerve resection. Using Solexa sequencing, computational analysis and Q-PCR verification, 93 novel miRNAs in rats were discovered and identified, of which 42 novel miRNAs were first reported in proximal sciatic nerve of rat and 51 novel miRNAs were produced at days 1, 4, 7 and 14 after sciatic nerve resection. These data provide an important resource relating to the role and regulation of miRNAs for future studies relating to peripheral nerve injury and regeneration. Keywords: Small RNA sequencing

2012-05-06 | GSE26753 | GEO

Integrated Analysis of Long Non-coding RNAs (LncRNAs) and mRNA Expression Profiles Reveals the Potential Role of LncRNAs in Skeletal Muscle Development of the Chicken.

Project description:Long non-coding RNAs (lncRNAs) play important roles in transcriptional and post-transcriptional regulation. However, little is currently known about the mechanisms by which they regulate skeletal muscle development in the chicken. In this study, we used RNA sequencing to profile the leg muscle transcriptome (lncRNA and mRNA) at three stages of skeletal muscle development in the chicken: embryonic day 11 (E11), embryonic day 16 (E16), and 1 day after hatching (D1). In total, 129, 132, and 45 differentially expressed lncRNAs, and 1798, 3072, and 1211 differentially expressed mRNAs were identified in comparisons of E11 vs. E16, E11 vs. D1, and E16 vs. D1, respectively. Moreover, we identified the cis- and trans-regulatory target genes of differentially expressed lncRNAs, and constructed lncRNA-gene interaction networks. In total, 126 and 200 cis-targets, and two and three trans-targets were involved in lncRNA-gene interaction networks that were constructed based on the E11 vs. E16, and E11 vs. D1 comparisons, respectively. The comparison of the E16 vs. D1 lncRNA-gene network comprised 25 cis-targets. We determined that lncRNA target genes are potentially involved in cellular development, and cellular growth and proliferation using Ingenuity Pathway Analysis. The gene networks identified for the E11 vs. D1 comparison were involved in embryonic development, organismal development and tissue development. The present study provides an RNA sequencing based evaluation of lncRNA function during skeletal muscle development in the chicken. Comprehensive analysis facilitated the identification of lncRNAs and target genes that might contribute to the regulation of different stages of skeletal muscle development.

| S-EPMC5220077 | biostudies-literature

Solexa sequencing of small RNAs in Sprague-Dawley (SD) rat [proximal sciatic nerve]

2012-05-06 | E-GEOD-26753 | biostudies-arrayexpress

Long noncoding RNAs (lncRNAs) in human lymphomas.

Project description:Lymphomas are a diverse group of haematologic malignancies, which occur in infection-fighting cells of the lymphatic system. Long non-coding RNAs (lncRNAs) are non-coding RNAs, which have recently received significant attention as the main mediators of gene expression. In this review, we summarize the current knowledge on lncRNAs involved in lymphomas, their molecular functions, as well as their potential clinical value. Relevant literature was identified by a PubMed search of English language papers using the following terms: Lymphoma, LncRNA, leukemia, proliferation, apoptosis, and prognosis. LncRNAs are imperative for lymphoma carcinogenesis through affecting apoptosis, cell proliferation, invasion, and response to chemotherapy. The expression level of lncRNAs can affect chemotherapy-induced apoptosis. Taken together, lncRNA dysregulation in lymphoma cells is not only an epiphenomenon but also lncRNA transcription is critically related to the initiation and progression of lymphomas. Aberrant expression of lncRNAs can lead to the transformation of normal lymphocytes into lymphoma cells.

| S-EPMC9170579 | biostudies-literature

Integrated analysis of mRNA and long noncoding RNA profiles in peripheral blood mononuclear cells of patients with bronchial asthma.

Project description:BackgroundBronchial asthma is a heterogeneous disease with distinct disease phenotypes and underlying pathophysiological mechanisms. Long non-coding RNAs (lncRNAs) are involved in numerous functionally different biological and physiological processes. The aim of this study was to identify differentially expressed lncRNAs and mRNAs in patients with asthma and further explore the functions and interactions between lncRNAs and mRNAs.MethodsTen patients with asthma and 9 healthy controls were enrolled in this study. RNA was isolated from peripheral blood mononuclear cells. We performed microarray analysis to evaluate lncRNA and mRNA expression. The functions of the differentially expressed mRNAs were analyzed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. A global signal transduction network was constructed to identify the core mRNAs. An lncRNA-mRNA network was constructed. Five mRNAs showing the greatest differences in expression levels or high degrees in the gene-gene functional interaction network, with their correlated lncRNAs, were validated by real-time quantitative polymerase chain reaction.ResultsWe identified 2229 differentially expressed mRNAs and 1397 lncRNAs between the asthma and control groups. Kyoto Encyclopedia of Genes and Genomes pathway analysis identified many pathways associated with inflammation and cell survival. The gene-gene functional interaction network suggested that some core mRNAs are involved in the pathogenesis of bronchial asthma. The lncRNA-mRNA co-expression network revealed correlated lncRNAs. CXCL8, FOXO3, JUN, PIK3CA, and G0S2 and their related lncRNAs NONHSAT115963, AC019050.1, MTCYBP3, KB-67B5.12, and HNRNPA1P12 were identified according to their differential expression levels and high degrees in the gene-gene network.ConclusionsWe identified the core mRNAs and their related lncRNAs and predicted the biological processes and signaling pathways involved in asthma.

| S-EPMC9059365 | biostudies-literature

Senescence-associated lncRNAs: senescence-associated long noncoding RNAs.

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.

| S-EPMC3773026 | biostudies-literature

Integrated analysis of long non-coding RNAs (lncRNAs) and mRNA expression profiles identifies lncRNA PRKG1-AS1 playing important roles in skeletal muscle aging.

Project description:This study aimed to identify long non-coding RNAs (lncRNAs) involving in the skeletal muscle aging process. Skeletal muscle samples from old and young subjects were collected for lncRNA-sequencing. Differentially expressed genes (DEGs) and DElncRNAs between young and old groups were identified and a co-expression network was built. Further, a dexamethasone-induced muscle atrophy cell model was established to characterize the function of a critical lncRNA. A total of 424 DEGs, including 271 upregulated genes and 153 downregulated genes as well as 152 DElncRNAs including 76 up-regulated and 76 down-regulated lncRNAs were obtained. Functional analysis demonstrated that the DEGs were significantly related to immune response. Coexpression network demonstrated lncRNA AC004797.1, PRKG1-AS1 and GRPC5D-AS1 were crucial lncRNAs. Their expressions were further validated by qRT-PCR in human skeletal muscle and the muscle atrophy cell model. Further in vitro analysis suggested that knock-down of PRKG1-AS1 could significantly increase cell viability and decrease cell apoptosis. qRT-PCR and western blot analyses demonstrated that knock-down of PRKG1-AS1 could increase the expression of MyoD, MyoG and Mef2c. This study demonstrated that lncRNAs of GPRC5D-AS1, AC004797.1 and PRKG1-AS1 might involve the aging-associated disease processes.

| S-EPMC8221296 | biostudies-literature

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