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Microarray technology provides a unique opportunity to examine gene expression patterns in human embryonic stem cells (hESCs). We performed a meta-analysis of 38 original studies reporting on the transcriptome of hESCs. We determined that 1,076 genes were found to be overexpressed in hESCs by at least three studies when compared to differentiated cell types, thus composing a “consensus hESC gene list.” Only one gene was reported by all studies: the homeodomain transcription factor  POU5F1 / OCT3 / 4 . The list comprised other genes critical for pluripotency such as the transcription factors  NANOG  and  SOX2 , and the growth factors  TDGF1 / CRIPTO  and  Galanin . We show that  CD24  and  SEMA6A , two cell surface protein-coding genes from the top of the consensus hESC gene list, display a strong and specific membrane protein expression on hESCs. Moreover, CD24 labeling permits the purification by flow cytometry of hESCs cocultured on human fibroblasts. The consensus hESC gene list also included the  FZD7  WNT receptor, the G protein-coupled receptor  GPR19 , and the  HELLS  helicase, which could play an important role in hESCs biology. Conversely, we identified 783 genes downregulated in hESCs and reported in at least three studies. This “consensus differentiation gene list” included the  IL6ST / GP130  LIF receptor. We created an online hESC expression atlas,  http://amazonia.montp.inserm.fr , to provide an easy access to this public transcriptome dataset. Expression histograms comparing hESCs to a broad collection of fetal and adult tissues can be retrieved with this web tool for more than 15,000 genes.

A Meta‐Analysis of Human Embryonic Stem Cells Transcriptome Integrated into a Web‐Based Expression Atlas