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| Status |
Public on Apr 01, 2021 |
| Title |
Co-expression Networks of mRNAs and non-coding RNAs of bones around implants in hyperlipidemic rats (RNA-seq data sets) |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Purpose: Hyperlipidemia has been shown to contribute to reduced implant osseointegration, but the underlying mechanism remains poorly understood. Recently, non-coding RNAs (ncRNAs) have been established as key regulators of various pathophysiological processes. Therefore, the current study aims to examine the expression profiles of mRNAs and ncRNAs in femoral tissues around surgical implants in a murine hyperlipidemia model via RNA sequencing.Materials and method: Twenty adult male Wistar rats were equally divided between an experimental group and a control group, which were fed a high-fat diet and a normal diet, respectively. Titanium root-form implants was inserted into both femoral shafts of each rat in eight weeks. Bone tissues were collected at day 10 after the insertion of the implants and subsequently used for RNA extraction and sequencing. The sequenced reads were refined, assembled and annotated to obtain mRNA, microRNA (miRNA), long non-coding RNA (lncRNA) and circular RNA (circRNA) transcripts. The levels of all types of RNA molecules in both animal groups were quantified and differentially expressed candidates were identified. The function of the identified RNAs were predicted by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. LncRNA-miRNA-mRNA and circRNA-miRNA-mRNA co-expression network of differentially expressed RNAs were constructed. Real-time polymerase chain reactions (RT-PCR) were performed to validate the expression levels of selected candidates.Results: The serum lipid levels of the experimental group were significant higher than those of the control group (p < 0.05). In total, 389 mRNAs, 73 miRNAs, 770 lncRNAs and 7 circRNAs were shown to be differentially expressed (p < 0.05, fold change > 2). GO analysis found that regulation of bone mineralization, negative regulation of chondrocyte differentiation and bone development changed significantly. The network that maybe related to osteogenesis included 6 mRNAs, 8 miRNAs, 6 circRNAs, 119 lncRNAs and 362 associations. Expression level of most RNAs detected by RT-PCR was consistent with that by RNA sequencing. Conclusion: Functional analysis predicted a panel of differentially expressed mRNAs and ncRNAs associated with osteogenesis. The results of the current study will greatly contribute to the elucidation of the mechanism for implant osseointegration under hyperlipidemia.
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| Overall design |
The expression profiles of mRNAs and non-coding RNAs of femur bones at 10 days after implantation in hyperlipidemic and normal rats
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| Contributor(s) |
Dong X, Lan J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Apr 23, 2018 |
| Last update date |
Apr 01, 2021 |
| Contact name |
Chen Jishuang |
| E-mail(s) |
biochenjs@njtech.edu.cn
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| Organization name |
Nanjing Tech University
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| Department |
College of Biotechnology and Pharmaceutical Engineering
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| Street address |
NO.30 Puzhu Road(S)
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
211800 |
| Country |
China |
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| Platforms (1) |
| GPL22396 |
Illumina HiSeq 4000 (Rattus norvegicus) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE113523 |
Co-expression Networks of mRNAs and non-coding RNAs of bones around implants in hyperlipidemic rats |
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| Relations |
| BioProject |
PRJNA451434 |
| SRA |
SRP142293 |
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