SEARCH

SEARCH BY CITATION

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

FilenameFormatSizeDescription
SC_12-0122_sm_supplFigure1.tif1476KSupplementary Figure 1. Genome-wide CpG methylation and gene expression profiling of ES, iPS and somatic cells of origin. (a) Two-dimensional scatter plots of Infinium methylation values in one representative sample of somatic cells versus their induced-pluripotent cells counterparts (left, keratinocytes; right, fibroblasts). (b) Two-dimensional scatter plots of Infinium methylation values in one representative sample of embryonic stem cell versus one representative induced-pluripotent cell sample (left, keratinocytes; right, fibroblasts). (c) Twodimensional scatter plots of genome wide expression profiles in one representative sample of somatic cells versus their induced-pluripotent cells counterparts (left, keratinocytes; right, fibroblasts). (d) Two-dimensional scatter plots of genome wide expression profiles in one representative sample of embryonic stem cell versus one representative induced-pluripotent cell sample (left, keratinocytes; right, fibroblasts).
SC_12-0122_sm_supplFigure2.tif1105KSupplementary Figure 2. Differentially methylated regions between iPS and ES cells. (a) Number of differentially hypermethylated CpGs unique and shared in KiPS and FiPS compared to ES cells. Fail to methylate corresponds to regions that were hypermethylated in ES but not in somatic and iPS cells. Aberrant undermethylation corresponds to probes that were hypermethylated in both somatic and ES cells but not in iPS cells. Fail to demethylate correspond to probes hypermethylated in somatic and iPS cells but not in ES cells. Aberrant hypermethylation corresponds to probes that were hypermethylated in iPS cells but not in ES and somatic cells. A CpG was considered as hypermethylated when at least a 70% of the replicates in each category has a b-value from BeadArray higher than 0.75. (b) Number of differentially hypomethylated CpGs unique and shared in KiPS and FiPS compared to ES cells. Fail to methylate corresponds to regions that were hypomethylated in somatic and iPS cells but not in ES cells. Aberrant hypomethylation corresponds to probes that were hypomethylated in iPS cells but not in ES and somatic cells. Fail to demethylate corresponds to probes hypomethylated in ES but not in somatic and iPS cells. Aberrant overmethylation corresponds to probes that were hypomethylated in somatic and ES cells but not iPS cells. A CpG was considered hypomethylated when its b-value from BeadArray was lower than 0.25 in at least 70% of the replicates in each category.
SC_12-0122_sm_supplFigure3.tif856KSupplementary Figure 3. Aberrant DNA methylation patterns at TCERGL1 gene. (a) Levels of DNA methylation in two different probes located at the regulatory regions of TCERGL1. The location of the probes relative to the TSS is indicated. (b) Expression levels of TCERGL1 determined by microarray analysis. Mean and standard deviation for each category of lines analyzed in this study relative to the expression in ES cells is shown. (c) Levels of expression of TCERGL1 reported in the indicated reprogramming experiments.
SC_12-0122_sm_supplFigure4.tif754KSupplementary Figure 4. Methylation levels at probes located in the X chromosome. Box plot representation of the DNA methylation levels at probes located in the X chromosome covered by the Infinium array.
SC_12-0122_sm_supplFigure5.tif544KSupplementary Figure 5. Promoter CpG methylation status of differentially methylated genes after reprogramming of fibroblasts (a) or keratinocytes (b). The location of the probe included in the methylation array is indicated by a red bar. CpG dinucleotides are represented as short vertical lines. Results of bisulfite genomic sequencing of 10 individual clones are shown. Presence of a methylated or unmethylated cytosine is indicated by a black or white square, respectively.
SC_12-0122_sm_supplFigure6.tif294KSupplementary Figure 6. Reprogramming efficiencies and methylation levels in tissue specific and pluripotency genes in fetal, extra-embryonic and adult cell types. (a) Reported reprogramming efficiencies of several cell types. References can be found in the main text (b) Box plot of methylation levels found in genes that are hypermethylated in ES cells in different cell types. (c) Box plot of methylation levels of the pluripotency genes in different cell types.
SC_12-0122_sm_supplFigure7.tif310KSupplementary Figure 7. mRNA levels of different DNMTs in the studied cell lines. Levels were determined by Q-PCR and plotted relative to GAPDH. Mean and standard deviation of triplicate measures are shown.
SC_12-0122_sm_supplTable1.pdf18KSupplementary Table 1. List of primers used in this study. A. Primers used for bisulfite sequencing reactions. B. Primers used to determine the levels of DNMTs expression by qPCR.
SC_12-0122_sm_supplTable2.xls92KSupplementary Table 2. Differentially hypermethylated probes between ES and KiPS cells. Fail to methylate corresponds to regions that were hypermethylated in ES but not in keratinocytes and KiPS cells. Aberrant undermethylation corresponds to probes that were hypermethylated in both keratinocytes and ES cells but not in KiPS cells. Fail to demethylate correspond to probes hypermethylated in keratinocytes and KiPS cells but not in ES cells. Aberrant hypermethylation corresponds to probes that were hypermethylated in KiPS cells but not in ES cells and keratinocytes. A CpG was considered as hypermethylated when at least a 70% of the replicates in each category has a b-value from BeadArray higher than 0.75.
SC_12-0122_sm_supplTable3.xls233KSupplementary Table 3. Differentially hypermethylated probes between ES and FiPS cells. Fail to methylate corresponds to regions that were hypermethylated in ES but not in fibroblasts and FiPS cells. Aberrant undermethylation corresponds to probes that were hypermethylated in both fibroblasts and ES cells but not in FiPS cells. Fail to demethylate correspond to probes hypermethylated in fibroblasts and FiPS cells but not in ES cells. Aberrant hypermethylation corresponds to probes that were hypermethylated in FiPS cells but not in ES cells and fibroblasts. A CpG was considered as hypermethylated when at least a 70% of the replicates in each category has a b-value from BeadArray higher than 0.75.
SC_12-0122_sm_supplTable4.xls52KSupplementary Table 4. Differentially hypomethylated probes between ES and KiPS cells. Fail to methylate corresponds to regions that were hypomethylated in keratinocytes and KiPS cells but not in ES cells. Aberrant hypomethylation corresponds to probes that were hypomethylated in KiPS cells but not in ES cells and keratinocytes. Fail to demethylate corresponds to probes hypomethylated in ES but not in keratinocytes and KiPS cells. Aberrant overmethylation corresponds to probes that were hypomethylated in keratinocytes and ES cells but not KiPS cells. A CpG was considered hypomethylated when its b-value from BeadArray was lower than 0.25 in at least 70% of the replicates in each category.
SC_12-0122_sm_supplTable5.xls94KSupplementary Table 5. Differentially hypomethylated probes between ES and FiPS cells. Fail to methylate corresponds to regions that were hypomethylated in fibroblasts and FiPS cells but not in ES cells. Aberrant hypomethylation corresponds to probes that were hypomethylated in FiPS cells but not in ES cells and fibroblasts. Fail to demethylate corresponds to probes hypomethylated in ES but not in fibroblasts and FiPS cells. Aberrant overmethylation corresponds to probes that were hypomethylated in fibroblasts and ES cells but not FiPS cells. A CpG was considered hypomethylated when its b-value from BeadArray was lower than 0.25 in at least 70% of the replicates in each category.
SC_12-0122_sm_supplTable6.xls397KSupplementary Table 6. List of sequences with methylation changes during in vitro induction of iPS from keratinocytes. A CpG was considered as hypermethylated when at least a 70% of the replicates in each category has a b-value from BeadArray higher than 0.75. BeadArray's data, including Entrez Gene ID, target ID in Infinium Assays, symbol, gene accession number, chromosome location and methylation beta values are indicated for each probe-set.
SC_12-0122_sm_supplTable7.xls179KSupplementary Table 7. List of sequences with methylation changes during in vitro induction of iPS from fibroblasts. A CpG was considered as hypermethylated when at least a 70% of the replicates in each category has a b-value from BeadArray higher than 0.75. BeadArray's data, including Entrez Gene ID, target ID in Infinium Assays, symbol, gene accession number, chromosome location and methylation beta values are indicated for each probe-set.

Please note: Wiley Blackwell is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.