StemCellDB: The Human Pluripotent Stem Cell Database at the National Institutes of Health

• Published in: Stem cell research 2013-01, Vol.10 (1), p.57-66
• Main Authors: Mallon, Barbara S., Chenoweth, Josh G., Johnson, Kory R., Hamilton, Rebecca S., Tesar, Paul J., Yavatkar, Amarendra S., Tyson, Leonard J., Park, Kyeyoon, Chen, Kevin G., Fann, Yang C., McKay, Ronald D.G.
• Format: Article
• Language: English
• Subjects: Animals; Cell fate; Cell Line; Databases, Factual; Gene Expression Profiling; Humans; Mice; National Institutes of Health (U.S.); Pluripotent Stem Cells - cytology; Pluripotent Stem Cells - metabolism; Principal Component Analysis; United States
• ISSN: 1873-5061; 1876-7753
• DOI: 10.1016/j.scr.2012.09.002

Much of the excitement generated by induced pluripotent stem cell technology is concerned with the possibility of disease modeling as well as the potential for personalized cell therapy. However, to pursue this it is important to understand the ‘normal’ pluripotent state including its inherent variability. We have performed various molecular profiling assays for 21 hESC lines and 8 hiPSC lines to generate a comprehensive snapshot of the undifferentiated state of pluripotent stem cells. Analysis of the gene expression data revealed no iPSC-specific gene expression pattern in accordance with previous reports. We further compared cells, differentiated as embryoid bodies in 2 media proposed to initiate differentiation towards separate cell fates, as well as 20 adult tissues. From this analysis we have generated a gene list which defines pluripotency and establishes a baseline for the pluripotent state. Finally, we provide lists of genes enriched under both differentiation conditions which show the proposed bias toward independent cell fates. [Display omitted] ► We introduce StemCellDB, a database of molecular profiles for twenty one hESCs. ► Our search engine allows simple interrogation of gene expression levels. ► No gene expression pattern was found to be unique to either hESCs or hIPSCs. ► We present a gene list of pluripotency-associated genes. ► We show two differentiation media direct cells toward independent cell fates.