lnc-SAMD14-4 can regulate expression of the COL1A1 and COL1A2 in human chondrocytes

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Bioinformatics and Genomics

Main article text

 

Introduction

Materials and Methods

Specimen collection

LncRNA and mRNA microarray analysis

RNA extraction and quantitative PCR

Cell culture and treatment

Cell transfection

Statistical analysis

Results

Analysis of differential expression among lncRNAs-mRNAs in OA

Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of dysregulated mRNAs

LncRNA-mRNA co-expression network

Verification of lncRNAs and mRNAs expression by qRT-PCR

Prediction of novel lncRNA targeting

COL1A1, COL1A2 and lnc-SAMD14-4 were highly expressed in the IL-1 β-treated human primary chondrocytes

lnc-SAMD14-4 was involved in IL-1 β-induced COL1A1 and COL1A2 expression in human primary chondrocytes

Discussion

Conclusion

Supplemental Information

The MIAME checklist

DOI: 10.7717/peerj.7491/supp-1

The quality control of total RNA

(A) the SDS-PAGE gels of total RNA. 28S ribosomal RNA and 18S ribosomal RNA bands appeared in all tissue samples (B) The electrophoresis pattern of SDS-PAGE of total RNA. (C) the analysis of SDS-PAGE of total RNA, RNA Integrity Number(RIN) >7 represent the quality of RNA can satisfy the study requirements.

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Prediction of putative proteins encoded by lnc-SAMD14-4 using ORF Finder

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The codon substitution frequency scores(CSF) of lnc-SAMD14-4

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QPCR analysis confirmed increased lnc-SAMD14-4 expression in human primary chondrocytes after pcDNA3.1 +-lnc-SAMD14-4 transfection

QPCR analysis confirmed increased lnc-SAMD14-4 expression in human primary chondrocytes after pcDNA 3.1+-lnc-SAMD14-4 transfection.

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The effect of three independent specifically targeting siRNA against lnc-SAMD14-4 was measured by QPCR

The strongest inhibitory result was achieved by lnc-SAMD14-4(2#)

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qPCR primers used in this study

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Differentially expressed lncRNA in OA and non-OA groups

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Differentially expressed mRNA in OA and non-OA groups

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Biological processes found with Go enrichment analysis for up-regulated mRNA in OA and non-OA groups

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The cellular process of Go enrichment analysis for up-regulated mRNA in OA and non-OA groups

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Molecular functions for Go enrichment analysis of up-regulated mRNA in OA and non-OA groups

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Biological processes for GO enrichment analysis of down-regulated mRNA in OA and non-OA groups

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Cellular process for GO enrichment analysis of down-regulated mRNA in OA and non-OA groups

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Molecular functions for GO enrichment analysis of down-regulated mRNA in OA and non-OA groups

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Pathway analysis of up-regulated mRNA in OA and non-OA groups

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Pathway analysis of down-regulated mRNA in OA and non-OA groups

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Dysregulated mRNAs enriched in the PI3K-Akt signal pathway

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The lncRNA-mRNA interaction pairs based on the PI3K-Akt signal pathway

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Top 500 correlations of lncRNA-mRNA interaction pairs based on the PI3K-Akt signal pathway

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Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Haibin Zhang conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Cheng Chen and Yinghong Cui conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Yuqing Li performed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper.

Zhaojun Wang performed the experiments, contributed reagents/materials/analysis tools.

Xinzhan Mao performed the experiments.

Pengcheng Dou, Yihan Li and Chi Ma performed the experiments, provided the study materials.

Human Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

This study was approved by the Ethics commission of the 163rd Central Hospital of the Chinese People’s Liberation Army (IRB. [2015] 001).

Microarray Data Deposition

The following information was supplied regarding the deposition of microarray data:

GEO: GSE113825.

Data Availability

The following information was supplied regarding data availability:

The raw data are included in the figures, tables, and Supplemental Tables.

Funding

The study was supported by the National Natural Science Foundation of China (#81201432, 81371997), the Army Medical Research Subject of the 12th Five-Year-Plan fund (#CWS11J275), the Scientific Research Fund of Hunan Provincial Education Department (#15B140), the Hunan Province Health and Life Committee Scientific Research Project (#B2016148), the Military Medical Science and Technology Youth Training Program (#2018JJ6033), and the Hunan Provincial Innovation Foundation for Postgraduates (#CX2015B185). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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