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STEM_3_sm_suppinfotable1.doc52KSupporting 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.pdf102KSupporting Information Table 2. Complete listing of Affymetrix probesets that show differential expression upon inhibition of PI3Ks in murine ES cells.
STEM_3_sm_suppinfotable3.pdf138KSupporting Information Table 3. Identity of the probesets contained within each k-means cluster.
STEM_3_sm_suppinfotable4.pdf51KSupporting 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.pdf49KSupporting 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.doc121KSupporting 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.pdf45KSupporting 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.pdf44KSupporting 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.pdf56KSupporting 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.pdf61KSupporting 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., [53]. 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.pdf273KSupporting 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.pdf90KSupporting 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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