Identification of long non-coding RNA involved in osteogenic differentiation from mesenchymal stem cells using RNA-Seq data

Genetics and Molecular Research : GMR
W Q SongW J Liu

Abstract

The aim of this study was to identify long non-coding RNA (lncRNA) associated with osteogenic differentiation from mesenchymal stem cells (MSCs) using high-throughput RNA sequencing (RNA-Seq) data. RNA-Seq dataset was obtained from the European Bioinformatics Institute (accession No. PRJEB4496), including two replicates each for immortalized mesenchymal stem cells iMSC#3 cultured in growth medium (GM) and differentiation medium (DM) for 28 days. The clean reads were aligned to a hg19 reference genome by Tophat and assembled by Cufflinks to identify the known and novel transcripts. RPKM values were calculated to screen for differentially expressed RNA. Novel lncRNA were screened based on various filter criteria. Subsequently, the underlying function of novel lncRNAs were predicted by functional annotation by ERPIN, a co-expression network was constructed by WGCNA and the KEGG pathway enriched by KOBAS. A total of 3171 RNA differentially expressed between the DM and GM groups (2597 mRNA and 574 lncRNA) were identified. Among the 574 differentially expressed lncRNA, 357 were known and 217 were novel lncRNA. Furthermore, 32 novel lncRNA were found to be miRNA precursors (including miR-689, miR-640, miR-601, and miR-544). A total of...Continue Reading

Citations

Mar 31, 2017·Molecular Genetics and Genomics : MGG·Zhihong MaXiufang Wang
Sep 5, 2019·Endocrine, Metabolic & Immune Disorders Drug Targets·Dijie LiAirong Qian
Mar 15, 2018·Stem Cells International·Shuping PengCijun Shuai
Mar 28, 2019·Bone & Joint Research·J ZhangF Guo
Feb 10, 2018·Oncology Letters·Guo-Dong YaoXiu-Bao Ren
Apr 6, 2019·World Journal of Stem Cells·Zhong-Yu XieHui-Yong Shen
Apr 27, 2021·Frontiers in Cell and Developmental Biology·Carmen LanzillottiFernanda Martini
Jun 6, 2021·BMC Genomics·Sébastien RiquierThérèse Commes

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