title: Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state.
abstract: Human embryonic stem cells (hESCs) are an important source of stem cells in regenerative medicine, and much remains unknown about their molecular characteristics. To develop a detailed genomic profile of ESC lines in two different species, we compared transcriptomes of one murine and two different hESC lines by massively parallel signature sequencing (MPSS). Over 2 million signature tags from each line and their differentiating embryoid bodies were sequenced. Major differences and conserved similarities between species identified by MPSS were validated by reverse transcription polymerase chain reaction (RT-PCR) and microarray. The two hESC lines were similar overall, with differences that are attributable to alleles and propagation. Human-mouse comparisons, however, identified only a small (core) set of conserved genes that included genes known to be important in ESC biology, as well as additional novel genes. Identified were major differences in leukemia inhibitory factor, transforming growth factor-beta, and Wnt and fibroblast growth factor signaling pathways, as well as the expression of genes encoding metabolic, cytoskeletal, and matrix proteins, many of which were verified by RT-PCR or by comparing them with published databases. The study reported here underscores the importance of cross-species comparisons and the versatility and sensitivity of MPSS as a powerful complement to current array technology.
authors.affiliation: Genome Institute of Singapore, 60 Biopolis Street, Genome#02-01, Singapore 138672.
authors.forename: Chia Lin
authors.initials: CL
authors.lastname: Wei
authors.forename: Takumi
authors.initials: T
authors.lastname: Miura
authors.forename: Paul
authors.initials: P
authors.lastname: Robson
authors.forename: Sai-Kiang
authors.initials: SK
authors.lastname: Lim
authors.forename: Xiu-Qin
authors.initials: XQ
authors.lastname: Xu
authors.forename: Mathia Yu-Chuan
authors.initials: MY
authors.lastname: Lee
authors.forename: Sanjay
authors.initials: S
authors.lastname: Gupta
authors.forename: Lawrence
authors.initials: L
authors.lastname: Stanton
authors.forename: Yongquan
authors.initials: Y
authors.lastname: Luo
authors.forename: Jacqui
authors.initials: J
authors.lastname: Schmitt
authors.forename: Scott
authors.initials: S
authors.lastname: Thies
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.forename: Irina
authors.initials: I
authors.lastname: Khrebtukova
authors.forename: Daixing
authors.initials: D
authors.lastname: Zhou
authors.forename: Edison T
authors.initials: ET
authors.lastname: Liu
authors.forename: Yi Jun
authors.initials: YJ
authors.lastname: Ruan
authors.forename: Mahendra
authors.initials: M
authors.lastname: Rao
authors.forename: Bing
authors.initials: B
authors.lastname: Lim
mesh_terms: D000818:Animals; D002460:Cell Line; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000235:genetics / Q000502:physiology*; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000096:biosynthesis* / Q000235:genetics; D039901:Totipotent Stem Cells / Q000502:physiology*; D014158:Transcription, Genetic / Q000235:genetics / Q000502:physiology*
chemical_list: D012333:RNA, Messenger