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

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sc-11-0884_sm_SupplFigure1.pdf156KSupplementary Figure 1. RNA microarray expression of HLA-A and -C in published induced pluripotent stem cell lines. The expression levels of HLA-A (red) and -C (blue) were analyzed in four different human embryonic stem cell (hESC) lines (hatched bars), six different fibroblast cell lines (horizontal lined bars) and their derived induced pluripotent stem (iPS) cell lines (solid bars). Expression pattern of published cell lines using the U133+2 DNA chip was compared to fibroblast cell lines and human ES and iPS cells lines from our laboratory using the Gene ST chip (Affymetrix). The y-axis represents the relative expression level of each gene. The x-axis groups the data by cell origin. BJ1, BJ2 BJ fibroblast are three different foreskin lines containing the telomerase gene; while FS is a foreskin fibroblast primary cell line, HIF indicates human embryonic fibroblasts; Derm indicates human neonatal dermal fibroblasts; MRC5 are primary fetal cells; NHD indicates normal human dermal fibroblasts. The hESC lines where HI-OGN, HUES 8, HSF1, H9 and HESC H9. The BJ1 cell line was originally designated BJ48 and its iPS cell line is BJ-iPS1. The HIF line was originally designated Hif Fib 44 and its iPS cell lines are HIF iPS3, HIF iPS10, HIF iPS20, HIF iPS30, and HIF iPS32, consecutively. Derm was originally designated Derm Fib and its iPS cells lines are hips clone 1, hips clone 2, and hips clone 3. BJ2 was originally designated BJ and its iPS cell lines are BJ hiP12, BJ hiPS 5, BJ hiPS 6, BJ hiPS 8, and BJ hiPS AFP 12. MRC5 was originally designated MRC5 40 and its iPS cell lines are MRC5 iPS 2 and MRC5 iPS 22. The NHD fibroblasts were originally designated NHDF and its iPS cell lines are HiPS 1, HiPS 5, HiPS 2, and HiPS 7. iPS BJ28 iPS BJ29 and iPS FS1 are lines generated in our lab. These are the same iPS cells lines used in our last paper 25.
sc-11-0884_sm_SupplFigure2.pdf354KSupplementary Figure 2. RNA microarray expression of MHC II in published induced pluripotent stem cell lines. The expression levels of HLA-DP, -DQ and -DR were analyzed in four different human embryonic stem cell (hESC) lines (hatched bars), six different fibroblast cell lines (horizontal lined bars) and their derived induced pluripotent stem (iPS) cell lines (solid bars) and compared to the levels of MHC-II in spleen (n=3, white bars). Cell lines are the same as represented in Supplementary Figure 1.
sc-11-0884_sm_SupplFigure3.tif754KSupplementary Figure 3. Expression levels of DNA binding proteins which bind to the promoter of HLA-A/B/C and beta 2 microglobulin. Microarray expression levels in fibroblasts and pluripotent stem cells (human ES and iPS cell lines) of two of the nuclear factors from each binding protein family that did not show different levels between the somatic and pluripotent stem cells. Cell lines are the same as represented in Supplementary Figure 1.
sc-11-0884_sm_SupplFigure4.pdf317KSupplementary Figure 4. Linear regression results showing correlation of expression. A) lineage regression graphs showing significant levels of correlation for HLA-A versus NFkB1 or RelA and β2M versus NFκB1 or RelA R2 values. B) Microarray expression levels of the 3 other members of the NFκB family of protein - c-REL, NFκB2 and RelB showing no patterns of expression.
sc-11-0884_sm_SupplFigure5.tif79KSupplementary Figure 5. Chromatin immunoprecipitation (ChIP) analysis of the β2M and HLA-B promoter with RelA. Chip analysis was used to determine the specific interaction between RelA (p65) protein to the promoters of β2M and HLA-B. qPCR analysis was performed on bound DNA from RelA and control antibodies experiments using primers that recognize the promoter regions of β2M and HLA-B. Unrelated control region on the LDL Receptor gene did not show any significant enrichment in all cell types. Data presented is the mean ± SEM of 4 experiments. Astericks denoted statistical significance p<0.05.
sc-11-0884_sm_SupplFigure6.tif396KSupplementary Figure 6. Down regulation of RelA and NFκB1 decreases the effect of IFNγ on β2M expression. hESCs were transfected with 2 different shRNAs against RelA and NFκB1. The transfected clones were incubated for 48 hours with IFNγ to induce MHC-I expression. A) Western blot illustrating the decrease in protein of RelA and NFκβ1 after knockdown with shRNAs compared to control clone with no knockdown. B) Shown in the graph are the fold changes found in the expression of β2M transcript in the various clones as compared to non-silenced control hESCs that were treated with IFNγ. Data presented is the mean ± SEM of 4 experiments performed in triplicate. Astericks denote statistical significant p<0.02.

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