(A) Schematic representation of reprogramming experiments performed with the STEMCCA lentiviral vector. This vector encodes the mouse reprogramming factors in the order of Oct4 (O), Klf4 (K), Sox2 (S), and cMyc (C). The four starting female human fibroblast lines are listed.
(B) As in (A) for the MIP- retroviral reprogramming approach with fibroblast line NHDF17914. The MIP-vector encodes the human reprogramming factors in the indicated order.
(C) Phase-contrast image of a representative STEMCCA-hiPSC colony.
(D) TRA1-60 (green) and NANOG (red) immunostaining of STEMCCA-hiPSC line E. Nuclei were detected with Dapi (blue).
(E) Graph summarizing real-time PCR data for transcript levels of endogenously expressed pluripotency genes in indicated cell lines. All values are relative to GAPDH expression.
(F) Bisulfite sequencing of promoter regions of NANOG and OCT4 in indicated cell lines.
(G) Analysis of MiP-based GFP expression at different steps of the reprogramming process. FACS analysis of GFP levels in MIP-retrovirally infected fibroblasts before puromycin selection demonstrating approximately 9% infection efficiency. Phase-contrast and GFP fluorescence images to the right indicate that almost all cells express GFP at day 5 of reprogramming upon puromycin selection. Resulting hiPSCs do not express GFP as shown in the GFP fluorescence image and the FACS analysis of MIP-hiPSC line 2 in the bottom row.
(H) Real-time PCR for ectopic expression from the MIP- (top) or STEMCCA- (bottom) reprogramming cassettes in indicated cell lines, relative to GAPDH expression.
(I) Teratoma formation with differentiation into all three germ layers in three representative hiPSC lines. See Fig S1 for additional data.

(A) FISH for XIST RNA (green) in the Dapi-stained fibroblast line NHDF 17430. The accumulation of XIST RNA on the Xi can be seen as focal nuclear enrichment of the RNA signal.
(B) FISH for XIST RNA (green) in the STEMCCA-hiPSC line E, merged with Dapi in the left image and overlaid with an immunostaining for NANOG (red) in the right image.
(C) The graph depicts the percentage of NANOG-positive cells with a single Xi-like accumulation of XIST RNA for various STEMCCA-hiPSC lines. Fibroblast origin is marked with gray scale indicators and passage of hiPSCs is indicated.
(D) As in (B) with NANOG in green and XIST RNA in red for MIP-hiPSC line 1. Scale bar denotes 10um.
(E) As in (C) for various MIP-hiPSC lines. See Fig S2 for additional data.

(A) NANOG immunostaining (red) combined with RNA FISH for ATRX nascent transcripts (green) in the Dapi-stained STEMCCA-hiPSC line 19. A pinpoint of ATRX marks the site of nascent transcription and occurs from only one X chromosome.
(B) The graph depicts the quantification of NANOG-positive cells with monoallelic, biallelic, or no ATRX expression for various STEMCCA-hiPSC lines at the indicated passage. Fibroblast origin is given as in Fig 2C.
(C) As in (A) for MIP-hiPSC line 1.
(D) As in (B) for various MIP-hiPSC lines.
(E) FISH for XIST RNA (red) and ATRX transcripts (green) in STEMCCA-hiPSC line G at passage 8 with Dapi staining the nucleus. The XIST RNA cloud signal does not overlap with the single ATRX signal.
(F) As in (E) for MIP-hiPSC line 5 at passage 3 with XIST RNA in green and ATRX transcripts in red.
(G) Immunostaining for H3K18ac (green) and FISH for XIST RNA (red) in STEMCCA-hiPSC line E at passage 8. Exclusion of the histone mark can be seen at the site of XIST RNA accumulation and was found in 96% of cells in the population indicating silencing of the entire XIST RNA-coated X in hiPSCs. Scale bar = 5um.
(H) As in (G), except that Xi exclusion of H3K4 me3 was analyzed. Exclusion of this histone mark was found in 92% of hiPSCs. See Fig S3 for additional data.

(A) Schematic representation of random XCI in fibroblasts and potential XCI states in female hiPSC lines.
(B) Analysis of allele-specific expression of XIST using restriction enzyme-sensitive SNPs. RNA from NHDF17914 fibroblasts and STEMCCA-hiPSC lines E and G (passages 8–9) derived from this fibroblast population was reverse transcribed and two regions of XIST surrounding different SNPs were amplified by PCR and analyzed with and without the respective restriction digest as indicated. SNPs were chosen such that the PCR product derived from the two X alleles are differentially cleaved as indicated. Note that fibroblasts express both XIST alleles, while hiPSC line G exclusively expresses one and line E the other allele.
(C) As in (B) except for allele-specific expression of ATRX.
(D) As in (B) except for allele-specific expression of PDHA1.
(E) A subclone of NHDF17914 fibroblasts obtained upon delivery of a lentiviral shRNA targeting p53 was reprogrammed with the STEMCCA approach and allele-specific expression of PDHA1 determined at different times of the reprogramming process using the same assay as in (D). This fibroblast subclone only expresses allele 2 and does not reactivate allele 1 during reprogramming.
(F) As in (B) but, allele-specific expression of XIST was analyzed upon differentiation of STEMCCA hiPSC lines E and G into neural precursors (NPCs), indicating that non-random XCI is preserved upon differentiation.
(G) As in (F) except for allele-specific expression of ATRX in hiPSC-derived NPCs. See Fig S4 for additional information.

(A) Immunostaining for EZH2 (green) and H3K27me3 (red) in NHDF17914 fibroblasts, nuclei were detected with Dapi. The proportion of cells with an Xi-like accumulation for H3K27me3 and EZH2 are given.
(B) Immunostaining for EZH2 (grey, from far-red channel), NANOG (green) and FISH for XIST RNA (red) in STEMCCA-hiPSC line G at passage 8.
(C) Proportion of NANOG-positive cells with an Xi-like accumulation of EZH2 for various MIP and STEMCCA-hiPSC lines at around passages 4–8. See Fig S5 for additional data.
(D) Real-time PCR data for EZH2 transcript levels in given cell types, normalized to GAPDH.
(E) Real-time PCR data for EZH2 transcript levels in early passage STEMCCA-hiPSCs upon treatment with scrambled siRNA controls (siControl) or siRNAs targeting EZH2 (siEZH2), normalized to GAPDH.
(F) Immunostaining for EZH2 in an early passage STEMCCA-hiPSC line upon transfection of control or EZH2 siRNAs. Cells are mosaic for depletion of EZH2 and arrowheads point to EZH2 Xi enrichment in cells with clear EZH2 knockdown.
(G) Immunostaining for histone H3K27me3 (red) and EZH2 (far-red, pseudocolored in cyan) in fibroblasts two days after transfection of a GFP-EZH2 overexpression plasmid. The zoom in suggests that higher global levels of EZH2 in fibroblasts do not lead to Xi-enrichment of EZH2.

(A) RNA FISH for XIST (green) and ATRX (red) transcripts in STEMCCA-iPS line G at passage 16. At this passage, many cells without XIST RNA clouds were found. Note that ATRX continues to be expressed from only one chromosome. At around passage 22, this hiPSC line lost XIST RNA expression and coating in almost all cells (data not shown).
(B) Analysis of allele-specific expression of PDHA1 in STEMCCA-hiPSC lines G and E at passage 22 (upon loss of XIST) using our SNP-based assay. NHDF17914 fibroblast analysis was added as reference for a cell line expressing both alleles of PDHA1. Upon XIST loss, both hiPSC lines continue to express only the PHDA1 allele that was active at earlier passage (compare with Fig 4D) and do not reactivate the other allele.
(C) X chromosome paint (green) in STEMCCA-hiPSC lines G at passage 22 to detect the presence of two X chromosomes. The combination of the X-paint with RNA polymerase II immunostaining (red) illustrated that one of the two X chromosomes labeled with arrowheads is completely excluded from RNA polymerase II staining indicative of an Xi.
(D) Bisulfite sequencing of promoter region of XIST in indicated cell lines. Half of the clones were completely methylated in female fibroblasts and early passage STEMCCA-hiPSC in agreement with the notion that XIST is silenced on the Xa and actively expressed from the Xi. Complete methylation was found in STEMCCA-hiPSC line G at passage 22, which has lost XIST expression, and our H9 hESC culture, which also lacks XIST expression but contains an Xi (data not shown).

(A) Schematic representation of the expected result in the reprogramming experiment with male and female DMD fibroblasts using in the STEMCCA approach.
(B) TRA1-60 (green) immunostaining and FISH for XIST RNA (red) in a representative female DMD-hiPSC line at passage 3. Nuclei were detected with Dapi (blue).
(C) Graph summarizing real-time PCR data for transcript levels of endogenously expressed pluripotency genes in indicated cell lines, relative to GAPDH expression.
(D) As in (C) for ectopic expression from the STEMCCA cassette and endogenous levels of SOX2.
(E) Bisulfite sequencing of promoter regions of NANOG and OCT4 in female DMD fibroblasts and the descendant hiPSC clone 158b.
(F) PCR analysis of DMD expression in female and male DMD-hiPSC clones. The wild-type and mutant alleles of DYSTROPHIN can easily be distinguished by size (1411 bp versus 716 bp). As expected, the male line (162) expressed only the mutant allele and only one of the two DYSTROPHIN alleles was transcribed in each female hiPSC line.
(G) SNP-based analysis of allele-specific expression of ATRX in female DMD fibroblasts, two descendant hiPSC clones (158b and 158e), and one male DMD hiPSC line (162f). Both ATRX alleles are present in fibroblasts, but only one can be detected in each female hiPSC line.