Additional Supporting Information may be found in the online version of this article.

sc-12-0498_sm_SupplFigure1.tif1977KFigure S1 – Genomic distributions of the Esrrb, Sox2 and Esrrb-Sox2 binding sites with respect to transcription start sites.Binding sites were annotated to the nearest transcription start site from the RefSeq annotation. (A) Esrrb binding sites (B) Sox2 binding sites (C) Esrrb-(2-8)bp-Sox2 binding sites. Random sites were sampled from the GFP control ChIP data. 10 random lists were generated and the frequency and the standard error is shown here (black bars)
sc-12-0498_sm_SupplFigure2.tif2457KFigure S2 – Cell-type specific ‘fingerprints’ were defined by collecting only genes that were significantly (adjusted p-value <0.05) up-regulated at least 3-fold, and no more than 2-fold up-regulated in any other cell-type. Microarray data was taken from the accessions GSE18507, GSE30056 and GSE32199.
sc-12-0498_sm_SupplFigure3.pdf857KFigure S3 – The five genes Peg10, Rhox9, Rhox6, Plac1 and Irs3 are all robustly expressed in the placenta. Gene expression data was taken from the GeneAtlas (Su et al., 2004). All of the genes are specific to the placenta, with the exception of Irs3 which is robustly expressed in placenta and brown adipose tissue.
sc-12-0498_sm_SupplFigure4.tif626KFigure S4 – Nr0b1 expression is only affected in Esrrb, Nanog, Pou5f1 and Sox2 shRNA knockdowns, but not in Tbx3 and Tcl1 knockdowns. Expression of the four genes Esrrb, Sox2, Pou5f1 (Oct-4) and Nr0b1 were taken from Microarray data GSE4679 (Ivanova et al., 2006).
sc-12-0498_sm_SupplFigure5.tif481KFigure S5 – Expression of Sox2 and Esrrb is tightly linked with Nr0b1 expression as TSC are differentiated. Microarray data was taken from GSE18507. Normalised expression is shown for the genes Esrrb, Sox2, Cdx2 and Nr0b1.
sc-12-0498_sm_SupplText.pdf11KSupplementary Data
sc-12-0498_sm_SupplTable1.xls46KSupplementary Table 1
sc-12-0498_sm_SupplTable2.xls119KSupplementary Table 2

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