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MPSS profiling of human embryonic stem cells - PubMed

  • ️Thu Jan 01 2004

Comparative Study

MPSS profiling of human embryonic stem cells

Ralph Brandenberger et al. BMC Dev Biol. 2004.

Abstract

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

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Figures

Figure 1
Figure 1

RT-PCR analysis (a), cumulative tpm (b) and tpm of known ES cell markers (c) is shown. Note that MPSS identifies most known markers of huES cells and expression is at high tpm levels. * – signature maps to >100 location in the genome (class 0); ** – artifactual (class 5) signature

Figure 3
Figure 3

RT-PCR for E-ras/RASP, FGFR1 and novel genes identified as enriched in undifferentiated ES cells is shown in Panel A and B. Localization of E-cadherin and β-catenin in undifferentiated ES cell is shown in Panel C. All of the genes identified by MPSS and tested were present in undifferentiated ES cells and most were significantly downregulated as cells differentiated. Note the high expression at the cell surface and low or undetectable levels of β-catenin in the nucleus.

Figure 2
Figure 2

Cytoband mapping of ES cell expressed genes and regions of relatively high and low transcription relative to the refseq database is shown. More detailed mapping information is presented in supplementary tables.

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