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Embryonic Stem Cells/Induced Pluripotent Stem Cells
Version of Record online: 15 JAN 2009
Copyright © 2009 AlphaMed Press
Volume 27, Issue 4, pages 764–775, April 2009
How to Cite
Storm, M. P., Kumpfmueller, B., Thompson, B., Kolde, R., Vilo, J., Hummel, O., Schulz, H. and Welham, M. J. (2009), Characterization of the Phosphoinositide 3-Kinase-Dependent Transcriptome in Murine Embryonic Stem Cells: Identification of Novel Regulators of Pluripotency. STEM CELLS, 27: 764–775. doi: 10.1002/stem.3
Author contributions: M.P.S.: conception and design, collection and assembly of data, data analysis and interpretation and manuscript writing; B.K.: collection and assembly of data, data analysis and interpretation; B.T.: collection and assembly of data, data analysis and interpretation; R.K.: data analysis and interpretation; J.V.: data analysis and interpretation; O.H.: collection and assembly of data; H.S.: data analysis and interpretation; M.J.W.: conception and design, financial support, data analysis and interpretation, manuscript writing and final approval of manuscript.
First published online in STEM CELLSExpress January 15, 2009.
- Issue online: 6 APR 2009
- Version of Record online: 15 JAN 2009
- Accepted manuscript online: 15 JAN 2009 12:00AM EST
- Manuscript Accepted: 9 DEC 2008
- Manuscript Received: 1 JUL 2008
- European Community sixth Framework program. Grant Number: FunGenES LSHG-CT-2003-503494
- Marie-Curie Actions and Biotechnology and Biological Sciences Research Council
Additional supporting information available online.
|STEM_3_sm_suppinfotable1.doc||52K||Supporting Information Table 1. The gene specific primers used in this study and the annealing temperature used in PCR reactions using these primers.|
|STEM_3_sm_suppinfotable2.pdf||102K||Supporting Information Table 2. Complete listing of Affymetrix probesets that show differential expression upon inhibition of PI3Ks in murine ES cells.|
|STEM_3_sm_suppinfotable3.pdf||138K||Supporting Information Table 3. Identity of the probesets contained within each k-means cluster.|
|STEM_3_sm_suppinfotable4.pdf||51K||Supporting Information Table 4. Identity of the probesets contained within each functional group defined following interrogation of the 469 down-regulated probes with the DAVID Gene Functional Classification tool.|
|STEM_3_sm_suppinfotable5.pdf||49K||Supporting Information Table 5. Identity of probesets corresponding to down-regulated transcripts that were not included in the Gene Functional Classification performed using DAVID.|
|STEM_3_sm_suppinfotable6.doc||121K||Supporting Information Table 6. The distribution of genes encoding transcriptional regulators and DNA binding proteins (Functional group 1 of down-regulated transcripts) to different k-means clusters.|
|STEM_3_sm_suppinfotable7.pdf||45K||Supporting Information Table 7. Identity of the probesets contained within each functional group defined following interrogation of the 177 up-regulated probes with the DAVID Gene Functional Classification tool.|
|STEM_3_sm_suppinfotable8.pdf||44K||Supporting Information Table 8. Identity of probesets corresponding to up-regulated transcripts that were not included in the Gene Functional Classification performed using DAVID.|
|STEM_3_sm_suppinfotable9.pdf||56K||Supporting Information Table 9. A. Identity of the PI3K target genes that have direct associations with Nanog. B. Identity of genes within the two functional groups defined following DAVID gene functional classification analyses of the probesets listed in A.|
|STEM_3_sm_suppinfotable10.pdf||61K||Supporting Information Table 10. Features of the Zscan4 family of SCAN-domain-containing zinc finger proteins. The ENSEMBL and NCBI identifiers are given, along with the gene names, corresponding to those defined by Falco et al., . Unigene identifiers for each gene are shown and the number of predicted transcript variants indicated. The percentage identity at protein and nucleotide levels are given and indicate the high levels of homology of members of this family.|
|STEM_3_sm_suppinfofigure1.pdf||273K||Supporting Information Figure S1. Validation of gene expression changes by quantitative RT-PCR. E14tg2a ES cells were cultured in the presence of LIF plus or minus 5 μM LY294002 for the times indicated. Expression of selected genes were analysed by quantitative RT-PCR and target gene expression was normalized relative to ?-actin levels. The averages and SEM of duplicate samples from each of three independent biological replicates are shown; * indicates P < 0.05, ** indicates P<0.005 and *** indicates P< 0.0005, in a Student's t-test.|
|STEM_3_sm_suppinfofigure2.pdf||90K||Supporting Information Figure S2. Nucleotide and protein sequence of Zscan4c The SCAN-B homology domain (aa 9-163) is underlined, with core residues (aa 53-87) indicated by bold typeface. Residues that share >51% identity with the SCAN consensus sequence are shaded in turquoise, while conserved amino acid differences are shaded pink. The 3 zinc-finger motifs (aa 396-418; 453-475 & 480-503, with pfam E-values of 9.8×10-6, 5.7×10-6 and 1.4×10-4) are highlighted in bold italic script, with conserved residues in red. The zinc finger motif with lower homology (aa 425-447) is in italics with conserved residues in blue. Green lines above the nucleotide sequence specify regions to which primers used in this study were designed and include (i) forward full-length cloning primer; (ii) forward qRT-PCR primer; (iii) reverse qRT-PCR primer and forward esiRNA primer; (iv) reverse esiRNA primer amd (v) reverse full-length cloning primer.|
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