MPSS profiling of human embryonic stem cells.
BACKGROUND
Pooled human embryonic stem cells (hESC) cell lines were profiled to obtain a comprehensive list of genes common to undifferentiated human embryonic stem cells.


RESULTS
Pooled hESC lines were profiled to obtain a comprehensive list of genes common to human ES cells. Massively parallel signature sequencing (MPSS) of approximately three million signature tags (signatures) identified close to eleven thousand unique transcripts, of which approximately 25% were uncharacterised or novel genes. Expression of previously identified ES cell markers was confirmed and multiple genes not known to be expressed by ES cells were identified by comparing with public SAGE databases, EST libraries and parallel analysis by microarray and RT-PCR. Chromosomal mapping of expressed genes failed to identify major hotspots and confirmed expression of genes that map to the X and Y chromosome. Comparison with published data sets confirmed the validity of the analysis and the depth and power of MPSS.


CONCLUSIONS
Overall, our analysis provides a molecular signature of genes expressed by undifferentiated ES cells that can be used to monitor the state of ES cells isolated by different laboratories using independent methods and maintained under differing culture conditions
Brandenberger
Ralph
R
National Institute on Aging; GRC; Laboratory of Neuroscience, 5600 Nathan Shock Drive; Room 4E02; Baltimore, MD 21224, USA. RBrandenberger@Geron.com
Khrebtukova
Irina
I
Thies
R Scott
RS
Miura
Takumi
T
Jingli
Cai
C
Puri
Raj
R
Vasicek
Tom
T
Lebkowski
Jane
J
Rao
Mahendra
M
D002454:Cell Differentiation / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods; D018076:DNA, Complementary / Q000235:genetics; D004622:Embryo, Mammalian / Q000166:cytology*; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental / Q000235:genetics; D006801:Humans; D013234:Stem Cells / Q000737:chemistry* / Q000378:metabolism*
D018076:DNA, Complementary