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Characterization of human embryonic stem cell lines by the International Stem Cell Initiative

Abstract

The International Stem Cell Initiative characterized 59 human embryonic stem cell lines from 17 laboratories worldwide. Despite diverse genotypes and different techniques used for derivation and maintenance, all lines exhibited similar expression patterns for several markers of human embryonic stem cells. They expressed the glycolipid antigens SSEA3 and SSEA4, the keratan sulfate antigens TRA-1-60, TRA-1-81, GCTM2 and GCT343, and the protein antigens CD9, Thy1 (also known as CD90), tissue-nonspecific alkaline phosphatase and class 1 HLA, as well as the strongly developmentally regulated genes NANOG, POU5F1 (formerly known as OCT4), TDGF1, DNMT3B, GABRB3 and GDF3. Nevertheless, the lines were not identical: differences in expression of several lineage markers were evident, and several imprinted genes showed generally similar allele-specific expression patterns, but some gene-dependent variation was observed. Also, some female lines expressed readily detectable levels of XIST whereas others did not. No significant contamination of the lines with mycoplasma, bacteria or cytopathic viruses was detected.

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Figure 1: Surface-antigen expression patterns of undifferentiated hES cells.
Figure 2: Expression profiles of the archetypal hES genes, NANOG, POU5F1(OCT4) and TDGF.
Figure 3: Pairwise correlation of expression of NANOG with that of all tested genes.
Figure 4: Two-way cluster analysis of hES cell lines with respect to gene expression.
Figure 5: Two-way cluster analysis of differentiated hES cell lines with respect to gene expression.
Figure 6: XIST expression in male and female hES cell lines.

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Acknowledgements

The International Stem Cell Initiative was sponsored and supported by the International Stem Cell Forum. Additional support from individual participants, and for elements of the project, was also provided by: A*STAR; Academy of Sciences of the Czech Republic; The Academy of Finland; Applied Biosystems; Axordia Ltd.; Bayer; Biotechnology and Biological Sciences Research Council, Centre for Cell Therapy and Tissue Repair, Charles University, Prague, Czech Republic; Chemicon now part of Millipore; Dutch Platform for Tissue Engineering; The Ellison Medical Foundation; Engineering and Physical Sciences Research Council; Embryonic Stem Cell International; GE Healthcare; The Helsinki University Central Hospital Research; Invitrogen Corporation; The Juvenile Diabetes Research Foundation; The Medical Research Council; The Ministry of Education, Culture, Sports, Science, & Technology of Japan; The National Institute for Biological Standards & Control; National Institutes of Health grants 9R24RR021314-04, 5R24RR018405, 5R24RR017498-04; One North East Regional Developmental Agency; The Shelby Cullom Davis Foundation; Stem Cell Network Canada; Stem Cells in Development and Disease; Swedish Research Council. We would like to thank the following for their invaluable assistance with the project: Marga van Rooijen, Hubrecht Laboratory; Christine Pigott, University of Sheffield; Ludmila Ruban, University of Sheffield; Katie Amps, University of Sheffield; Nicholas Jenkins, University of Sheffield; Jeff Jones, WiCell Research Institute; Nancy Block, WiCell Research Institute. We are also grateful to D. Melton and C. Cowan, Harvard University/Howard Hughes Medical Institute, respectively, for making available the human ES cell lines HUES1-17 and to the ES Cell International Pte Ltd. for human ES cell lines HES1-6.

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Correspondence to Peter W Andrews.

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Competing interests

P.W.A. and B.B.K. receive royalty payments from the Wistar Institute in connection with the nonexclusive commercial licenses issued by the Institute for several of its monoclonal antibodies used in the present study (B.B.K.: SSEA1, SSEA3, SSEA4; P.W.A.: TRA antibodies). A.J.R., T.S. and E.S. are employees of Novocell, Inc., which is a for-profit company involved in commercializing human ES cell–derived products.

Supplementary information

Supplementary Fig. 1

Representative flow cytometry data for antigens expressed in the undifferentiated hES cells. (PDF 63 kb)

Supplementary Fig. 2

Histological Review - examples of histological sections from xenograft tumours submitted for analysis in the ISCI study. (PDF 260 kb)

Supplementary Table 1

Antibodies used in the FACS study. (PDF 80 kb)

Supplementary Table 2

Flow Cytometry Data. (XLS 601 kb)

Supplementary Table 3

Gene assayed by Low Density Array based Q-PCR. (PDF 80 kb)

Supplementary Table 4

Summary of gene expression results determined by quantitative PCR using Taqman Low-density arrays. (XLS 917 kb)

Supplementary Table 5

Imprinting Data Summary. (XLS 99 kb)

Supplementary Table 6

Cell lines and sample codes used in the ISCI study. (XLS 60 kb)

Supplementary Table 7

hES Cell Line availability. (PDF 76 kb)

Supplementary Table 8

Imprinted gene expression primers. (XLS 18 kb)

Supplementary Methods (PDF 230 kb)

Supplementary Note (PDF 827 kb)

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The International Stem Cell Initiative. Characterization of human embryonic stem cell lines by the International Stem Cell Initiative. Nat Biotechnol 25, 803–816 (2007). https://doi.org/10.1038/nbt1318

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