title: Comparison of microarray and RNA-Seq analysis of mRNA expression in dermal mesenchymal stem cells.
abstract: OBJECTIVE
  We characterized mRNA expression profiles in normal and psoriatic human dermal mesenchymal stem cells (DMSCs) to provide a reference for future investigation of differential gene expression in DMSCs.
  
  
  RESULTS
  Microarray and RNA sequencing (RNA-Seq) analyses both identified 23 differentially expressed genes using both platforms. The results showed comparable upregulation or downregulation for 14/23 genes using either platform and a 100 % coincidence rate was found by real-time PCR. For all of the differentially expressed genes that were verified by real-time PCR, the coincidence rate for RNA-Seq and real-time PCR was significantly higher than that for microarray analysis and real-time PCR (83.3 vs. 37.5 %, P < 0.0001). Furthermore, RNA-Seq revealed the presence of over 2300 novel transcription tags.
  
  
  CONCLUSIONS
  Relative to microarray analysis, RNA-Seq is more accurate in identifying differentially expressed genes in DMSCs.
authors.affiliation: Taiyuan City Centre Hospital, Institute of Dermatology, No. 1 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, Shanxi Province, China.
authors.forename: Junqin
authors.initials: J
authors.lastname: Li
authors.affiliation: Taiyuan City Centre Hospital, Institute of Dermatology, No. 1 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, Shanxi Province, China.
authors.forename: Ruixia
authors.initials: R
authors.lastname: Hou
authors.affiliation: Taiyuan City Centre Hospital, Institute of Dermatology, No. 1 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, Shanxi Province, China.
authors.forename: Xuping
authors.initials: X
authors.lastname: Niu
authors.affiliation: Taiyuan City Centre Hospital, Institute of Dermatology, No. 1 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, Shanxi Province, China.
authors.forename: Ruifeng
authors.initials: R
authors.lastname: Liu
authors.affiliation: Taiyuan City Centre Hospital, Institute of Dermatology, No. 1 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, Shanxi Province, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Laboratory Animal Center, Shanxi Medical University, No. 56 Xinjian Road South, Taiyuan, 030001, Shanxi Province, China.
authors.forename: Chunfang
authors.initials: C
authors.lastname: Wang
authors.affiliation: Taiyuan City Centre Hospital, Institute of Dermatology, No. 1 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, Shanxi Province, China.
authors.forename: Xinhua
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Dermatology, General Hospital of TISCO, No 23 Baiyangshu Street, Taiyuan, 030003, Shanxi Province, China.
authors.forename: Zhongping
authors.initials: Z
authors.lastname: Hao
authors.affiliation: Taiyuan City Centre Hospital, Institute of Dermatology, No. 1 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, Shanxi Province, China.
authors.forename: Guohua
authors.initials: G
authors.lastname: Yin
authors.affiliation: Taiyuan City Centre Hospital, Institute of Dermatology, No. 1 Dong San Dao Xiang, Jiefang Road, Taiyuan, 030009, Shanxi Province, China. zhangkaiming@sina.com.
authors.forename: Kaiming
authors.initials: K
authors.lastname: Zhang
mesh_terms: D000328:Adult; D002478:Cells, Cultured; D002681:China; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D006801:Humans; D008297:Male; D059630:Mesenchymal Stem Cells / Q000166:cytology* / Q000473:pathology; D011565:Psoriasis / Q000235:genetics* / Q000473:pathology; D017423:Sequence Analysis, RNA / Q000379:methods*
keywords: Dermal mesenchymal stem cells; Differential gene expression; Mesenchymal stem cells; Microarray; RNA sequencing