Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA Sequencing Facilitates Quantitative Analysis of Schwann cells Transcriptomes

ABSTRACT: Purpose: Whole-transcriptome sequencing technology and bioinformatics analysis were applied to systematically analyze the differentially expressed mRNAs, lncRNAs and miRNAs in SCs from DPN rats and control rats. Methods: mRNA, lncRNA and miRNA profiles of Schwann cells from DPN rats and control rats were generated by RNA sequencing, using Illumina Xten. The sequence reads that passed quality filters were analyzed at the transcript isoform level by using sequence analysis programs, including HISAT, Stringtie and DESeq2. qRT–PCR validation was performed using Takara, Vazyme and Clontech kits. Results: The data showed that 2925 mRNAs, 164 lncRNAs and 49 miRNAs were significantly differently expressed in SCs from DPN rats compared with control rats, with a fold change ≥1.2 or ≤ 0.833 and p value <0.05 . The results of qRT-PCR confirmed 13 mRNAs, 7 lncRNAs and 7 miRNAs which were consistent with the RNA-seq data. Functional and pathway analyses revealed that many enriched biological processes of GO terms and pathways were relevant to the function of SCs and the pathogenesis of DPN. Our study is the first to detect and analyze mRNAs, lncRNAs and miRNAs changes in Schwann cells from STZ-treated rats with DPN and reveal the novel interactions between dysregulated RNAs and the pathogenesis of DPN. Our data show that dysregulated RNAs have complicated interactions between them and play critical roles in regulating functions of SCs involved in the pathogenesis of DPN

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE142785 | GEO | 2020/01/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Analysis of altered lncRNA and mRNA expression profiles in the streptozotocin-induced diabetic rats compared to normal SD rats

Project description:Diabetes mellitus (DM) is one of the most common chronic diseases around the world, and diabetic peripheral neuropathy (DPN) is one of the most common complications of DM. We used microarrays to identify the differentially expressed lncRNAs and mRNAs in dorsal root ganglia (DRG) tissues from streptozotocin (STZ)-induced diabetic rats, taking normal SD rats as controls, and tried to find out the related genes which may be involved in the development of DPN.

2018-03-23 | GSE110233 | GEO

The long noncoding RNA expression profile of human intervertebral disc degeneration identified by microarray analysis

Project description:In addition to the well-known short noncoding RNAs as miRNAs, increasing evidence suggests that long noncoding RNAs (lncRNAs) act as key regulators in a wide aspect of biologic processes. Dysregulated expression of lncRNAs has been demonstrated being implicated in a variety of human diseases. However, there is relative paucity of information regarding the role of lncRNAs in intervertebral disc degeneration (IDD) hitherto. We have addressed the expression profiles of miRNAs in IDD previously. To determine whether lncRNAs is differentially expressed in IDD, we employed a lncRNA-mRNA microarray analysis of human nucleus pulposus (five degenerative as IDD and five normal specimens as control). With abundant probes accounting for 33,045 lncRNAs and 30,215 coding transcripts in our microarray, microarray data profiling indicated that 18995 lncRNAs and 14635 mRNAs were detected in all samples with 2309 lncRNAs and 3017 mRNAs differentially expressed in degenerated samples. Amongst them, 164 lncRNAs (97 up and 67 down) and 265 mRNAs were highly differentially expressed with an absolute fold change greater than ten. The upregulated mRNAs included the extracellular matrix components as COL1A2, LUM, FN1ACAN, DCN and ITFG2. 1100 lncRNAs and 1379 mRNAs were altered in the same direction in at least 4 of the 5 degenerative samples with fold change greater than 2 respectively. Three lncRNAs were chosen for the real-time quantitative PCR (qRT-PCR) analysis. qRT-PCR results showed a high consistency with the microarray data. In this study, to explore the potential involvement of lncRNAs in IDD, we conducted lncRNA and mRNA profiling in 5 human control nucleus pulposus tissue and 5 degenerative nucleus pulposus tissue by microarray.Biological replicates: 5 control, 5 degenerated, independently harvested.

2014-11-17 | E-GEOD-56081 | biostudies-arrayexpress

Transcriptome analysis of eosinophilic and noneosinophilic chronic rhinosinusitis with nasal polyps reveals distinct lncRNA expression profiles

Project description:Background: The pathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP) remains unclear. Long noncoding RNAs (lncRNAs) play pivotal roles in various biological processes, but their roles in CRSwNP have not been explored. We performed systematic transcriptome analysis of mRNAs and lncRNAs of eosinophilic and noneosinophilic CRSwNP to deepen our understanding of the disease mechanism. Methods: We analyzed expression profiles of mRNAs and lncRNAs with next-generation high-throughput RNA sequencing in patients with eosinophilic CRSwNP (n=3), noneosinophilic CRSwNP (n=3), and healthy control subjects (n=3). Results were verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR) in an independent cohort of patients. The dysregulated mRNAs and lncRNAs were identified and characterized via bioinformatics analysis. Results: A total of 1917 novel lncRNA transcripts and 280 known lncRNA transcripts were identified. Sample groups were separated by unsupervised hierarchical clustering on differentially expressed lncRNAs or mRNAs. The qRT-PCR results of five dysregulated lncRNAs were consistent with the RNA-seq data. The dysregulated genes were significantly overrepresented in immune response and extracellular environment related terms in Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The predicted functions of dysregulated lncRNAs were highly consistent with those of dysregulated mRNAs. Conclusion: The cross talk between inflammation and immune response and microenvironment is the key pathogenesis mechanism of CRSwNP. Patients with eosinophilic CRSwNP compared with noneosinophilic CRSwNP has distinct gene expression profiles. This highlights the necessity of designing personalized therapeutic strategies and suggests developing specific molecular biomarkers.

2017-02-14 | GSE72713 | GEO

RNA-seq analysis lncRNA and mRNA between crushed sciatic nerves and intact contralateral nerves

Project description:To investigate the potential function of lncRNAs in Schwann cell (SCs) response to sciatic nerve damage and repair, we extracted the total RNA of crushed sciatic nerves and intact contralateral nerves for RNA-sequencing (RNA-seq). A total of 98 differentially expressed lncRNAs (including 46 up-regulated and 52 down-regulated lncRNAs) and 77 differentially expressed mRNAs (including 55 up-regulated and 22 down-regulated mRNAs) were identified between crushed sciatic nerves and normal control (log 2 FC > 1 and p < 0.001).

2022-07-06 | GSE149657 | GEO

The long noncoding RNA expression profile of human intervertebral disc degeneration identified by microarray analysis

2014-11-17 | GSE56081 | GEO

Distinct mRNA and Long Non-coding RNAs (lncRNAs) Expression Profiles of Decidual Natural Killer Cells in Human Early Missed Abortion

Project description:Our present study analyzes decidual natural killer(dNK) cells expression profiles of the lncRNA and mRNA in missed abortional patients. A total of 276 mRNAs and 67 lncRNAs were identified to be significantly dysregulated in missed abortion (p<0.01). Subsequently, the potential function of dysregulated mRNAs and lncRNAs in missed abortion were explored through the bioinformatics method. In addition, the relationship between these dysregulated lncRNAs and mRNAs was revealed through constructing the lncRNA-mRNA interaction network. Our data showed that upregulated mRNAs were enriched in immune response and cytokine-cytokine receptor interaction while downregulated mRNAs were mainly related to cell adhesion and ECM-receptor interaction. Most importantly, several novel lncRNAs in dNKs, regulating core maternal-fetal interface activation-related mRNAs, were algorithmically predicted, indicating involvement of lncRNAs in the pathogenesis in early missed abortion.Topology analysis of lncRNA-mRNA interaction network suggested that the network presented a small world property, which means that most of mRNAs in the network were regulated by relative small number of hub lncRNAs. This study paves the way of investigating pathogenesis of early human missed abortion and facilitating the development of novel missed abortion therapeutics targeting lncRNAs.

2020-10-15 | GSE139087 | GEO

LncRNA and mRNA expression profiles from human GES-1 cells in response to Helicobacter pylori infection

Project description:Research on lncRNAs expression profiles in human interactions with Helicobacter pylori (H.pylori) is rare reported. We used HTA2.0 to investigate the expression changes of lncRNAs and mRNAs in human gastric epithelial cells (GES-1 cell line) infected with or without H.pylori infection. Our study provided a preliminary exploration of lncRNAs expression profiles in H.pylori-infected cell models by microarray. A subset of aberrantly expressed lncRNAs was verified by qRT-PCR. These dysregulated lncRNAs might contribute to the pathological processes during H.pylori infection. We infected GES-1 cells with H.pylori as experimental groups,and cells without H.pylori infection were regarded as control groups. After 24hr-infection, cells of each group were selected for total RNA extraction and hybridization on Affymetrix HTA2.0 arrays. The aberrant expression profiles of lncRNAs and mRNAs were explored by microarray analysis between experimental and control groups.

2015-11-03 | E-GEOD-74577 | biostudies-arrayexpress

High-throughput sequencing analyses of transcript changes in growth plates upon dexamethasone treatment

Project description:Glucocorticoid-induced growth retardation (GIGR) is a common adverse effect of glucocorticoid treatment in pediatric patients. Accumulating evidence indicates that non-coding RNAs (ncRNAs) are involved in the pathogenesis of GIGR, but the roles of specific ncRNAs in growth remain largely unknown. In this study, we established an in vivo GIGR rat model by 7- or 14- day dexamethasone (Dex) treatment and performed high-throughput RNA sequencing to identify mRNAs, lncRNAs, circRNAs, and miRNAs differentially expressed in GIGR rats relative to control rats in the growth plates.High-throughput RNA sequencing identified 1718 mRNAs, 896 lncRNAs, 60 circRNAs, and 72 miRNAs with differing expression levels at 7d group. At 14d group, 1515 mRNAs, 880 lncRNAs, 46 circRNAs, and 55 miRNAs with differential expression were identified. Eight mRNAs were validated by RT-qPCR, with expression level differences consistent with RNA sequencing data. Function enrichment analyses indicate that the PI3K-Akt signaling pathway, NF-kappa B signaling pathway, and TGF-beta signaling pathway participated in the development of the GIGR. Then, ceRNA networks were constructed to investigate the potential molecular mechanisms of ncRNAs. These results provide new insights for exploring the molecular mechanisms underlying GIGR.

2022-12-01 | GSE190744 | GEO

Identifying long non-coding RNAs in triple-negative breast cancer

Project description:We investigated the expression patterns of lncRNAs and mRNAs from TNBC tissues and matched histological normal breast tissues with Agilent Human lncRNA array V4.0 (4 × 180 K), which include 78,243 human lncRNAs and 30,215 coding transcripts. We identified 1,758 lncRNAs and 1,254 mRNAs that were differentially expressed (≥ 2-fold change), indicating that many lncRNAs are significantly upregulated or downregulated in TNBC. Among these, XR_250621.1 and NONHSAT011259 were the most unregulated and down regulated lncRNAs. qRT-PCR was employed to validate the microarray analysis findings, and results were consistent with the data from the microarrays. GO analysis and KEGG pathway analysis were applied to explore the potential lncRNAs functions, and some pathways including microtubule motor activity and DNA replication were identified in TNBC pathogenesis.

2015-08-01 | E-GEOD-64790 | biostudies-arrayexpress

The profiles of circRNAs, lncRNAs and mRNAs in drug-resistant non-small-cell lung cancer cell lines by RNA sequencing

Project description:We detected the expression profiles ofcircRNAs, lncRNAs and mRNAs in two drug-resistant NSCLC cell lines (A549/R and HCC827/R) and their parent cell lines (A549 and HCC827) by RNA sequencing, employed a comprehensive analysis of the dysregulated lncRNAs, miRNAs and mRNAs by bioinformatics methods.

2020-04-06 | GSE132418 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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