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Comparative transcriptome analysis of embryonic and adult stem cells with extended and limited differentiation capacity

Fernando Ulloa-Montoya1,2,3†, Benjamin L Kidder1†, Karen A Pauwelyn1,3, Lucas G Chase1, Aernout Luttun1,3, Annelies Crabbe3, Martine Geraerts3, Alexei A Sharov4, Yulan Piao4, Minoru SH Ko4, Wei-Shou Hu2 and Catherine M Verfaillie1,3*

1 Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA

2 Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA

3 Stamcel Instituut, Katholieke Universiteit Leuven, Leuven 3000, Belgium

4 Developmental Genomics and Aging Section, Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA

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Genome Biology 2007, 8:R163 doi:10.1186/gb-2007-8-8-r163

Published: 6 August 2007

Additional files

Additional data file 1:

Supplementary Table 1 lists genes expressed in MAPC at levels at least twofold higher than in MSC and ESC; supplementary Table 2 lists genes expressed in MAPC and ESC at levels at least twofold higher than in MSC; supplementary Table 3 lists genes expressed in MAPC and MSC at levels at least twofold higher than in ESC; supplementary Table 4 lists genes expressed in MAPC at levels at least twofold higher than in ESC and NS; supplementary Table 5 lists genes expressed in MAPC and ESC at levels at least twofold higher than in NS; supplementary Table 6 lists genes expressed in MAPC at levels at least twofold higher than in ESC in NIA microarrays; supplementary Table 7 lists genes expressed in ESCs at levels at least twofold higher than in MAPC in NIA microarrays; supplementary Table 8 contains a MAPC gene cluster comparison between Affymetrix and NIA microarrays; supplementary Table 9 lists genes differentially expressed between MSCs and MSC-like cells; supplementary Table 10 lists genes correlated with Pdgfra with twofold differential expression between all MAPC conditions cultured cells vs ESCs and MSCs; supplementary Table 11 lists genes anti-correlated to Pdgfra with a twofold differential expression between all MAPC conditions cultured cells vs ESCs and MSCs; supplementary Table 12 lists genes with at least twofold higher expression in rMAPC-1 than in rClone-2; supplementary Table 13 lists genes with at least twofold higher expression in rClone-2 than in rMAPC-1; supplementary Table 14 lists common differentially expressed genes in both mMAPC vs MSC and rMAPC-1 vs rClone-2 comparisons.

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Additional data file 2:

Supplementary Figure 1 shows PCA of MSC, MSC-like (MSC-l, mClone-3), MAPC-1 (M-1), MAPC-2 (M-2) and ESC on reported ESC and MSC hypoxia upregulated genes; supplementary Figure 2 shows PCA and NMF analysis of MSC, MSC-like (MSC-l, mClone-3), MAPC-1 (M-1), MAPC-2 (M-2) and ESC on differentially expressed genes minus genes correlated or anticorrelated to Pdgfra; supplementary Figure 3 shows the correlation of fold difference on common differentially expressed genes between mMAPCs vs MSCs and rMAPC-1 vs rClone-2.

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