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Reference maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines

ABSTRACT: The developmental potential of human pluripotent stem cells suggests that they can produce disease-relevant cell types for biomedical research. However, substantial variation has been reported among pluripotent cell lines, which could affect their utility and clinical safety. Such cell-line specific differences must be better understood before one can confidently use embryonic stem (ES) or induced pluripotent stem (iPS) cells in translational research. Towards this goal we have established genome-wide reference maps of DNA methylation and gene expression for 20 previously derived human ES lines and 12 human iPS cell lines, and we have measured the in vitro differentiation propensity of these cell lines. This resource enabled us to assess the epigenetic and transcriptional similarity of ES and iPS cells and to predict the differentiation efficiency of individual cell lines. The combination of assays yields a scorecard for quick and comprehensive characterization of pluripotent cell lines. We used microarrays to compare the gene expression profiles between human ES cell lines, iPS cell lines, fibroblasts and embryoid bodies, and to identify cell-line specific outlier genes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE25970 | GEO | 2011/02/03

SECONDARY ACCESSION(S): PRJNA135443

REPOSITORIES: GEO

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Reference maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines

Project description:The developmental potential of human pluripotent stem cells suggests that they can produce disease-relevant cell types for biomedical research. However, substantial variation has been reported among pluripotent cell lines, which could affect their utility and clinical safety. Such cell-line specific differences must be better understood before one can confidently use embryonic stem (ES) or induced pluripotent stem (iPS) cells in translational research. Towards this goal we have established genome-wide reference maps of DNA methylation and gene expression for 20 previously derived human ES lines and 12 human iPS cell lines, and we have measured the in vitro differentiation propensity of these cell lines. This resource enabled us to assess the epigenetic and transcriptional similarity of ES and iPS cells and to predict the differentiation efficiency of individual cell lines. The combination of assays yields a scorecard for quick and comprehensive characterization of pluripotent cell lines. We used microarrays to compare the gene expression profiles between human ES cell lines, iPS cell lines, fibroblasts and embryoid bodies, and to identify cell-line specific outlier genes. 20 human ES cell lines (HUES1, HUES3, HUES6, HUES8, HUES9, HUES13, HUES28, HUES44, HUES45, HUES48, HUES49, HUES53, HUES62, HUES63, HUES64, HUES65, HUES66, H1, H7, H9), 12 human iPS cell lines (hiPS 11a, hiPS 11b, hiPS 11c, hiPS 15b, hiPS 17a, hiPS 17b, hiPS 18a, hiPS 18b, hiPS 18c, hiPS 20b, hiPS 27b, hiPS 27e), 6 fibroblast cell lines (hFib 11, hFib 15, hFib 17, hFib 18, hFib 20, hFib 27), 5 embryoid bodies (hEB16d HUES1, hEB16d HUES3, hEB16d HUES6, hEB16d HUES45, hEB16d H1)

2011-02-03 | E-GEOD-25970 | biostudies-arrayexpress

Donor dependent variations in hematopoietic differentiation among embryonic and induced pluripotent stem cell lines.

Project description:Hematopoiesis generated from human embryonic stem cells (ES) and induced pluripotent stem cells (iPS) are unprecedented resources for cell therapy. We compared hematopoietic differentiation potentials from ES and iPS cell lines originated from various donors and derived them using integrative and non-integrative vectors. Significant differences in differentiation toward hematopoietic lineage were observed among ES and iPS. The ability of engraftment of iPS or ES-derived cells in NOG mice varied among the lines with low levels of chimerism. iPS generated from ES cell-derived mesenchymal stem cells (MSC) reproduce a similar hematopoietic outcome compared to their parental ES cell line. We were not able to identify any specific hematopoietic transcription factors that allow to distinguish between good versus poor hematopoiesis in undifferentiated ES or iPS cell lines. However, microarray analysis showed genes differentially expressed in ES and iPS cell lines according to their hematopoietic potential. These results demonstrate the influence of genetic background in variation of hematopoietic potential rather than the reprogramming process.

2015-11-17 | GSE75051 | GEO

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells (Affymetrix)

Project description:Knowledge of both the global chromatin structure and the gene expression programs of human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells should provide a robust means to assess whether the genomes of these cells have similar pluripotent states. Recent studies have suggested that ES and iPS cells represent different pluripotent states with substantially different gene expression profiles. We describe here a comparison of global chromatin structure and gene expression data for a panel of human ES and iPS cells. Genome-wide maps of nucleosomes with histone H3K4me3 and H3K27me3 modifications indicate that there is little difference between ES and iPS cells with respect to these marks. Gene expression profiles confirm that the transcriptional programs of ES and iPS cells show very few consistent differences. Although some variation in chromatin structure and gene expression was observed in these cell lines, these variations did not serve to distinguish ES from iPS cells. Examination of gene expression in 7 human ES cell lines, 8 human iPS cell lines, and 2 fibroblast cell line2.

2010-08-09 | E-GEOD-23402 | biostudies-arrayexpress

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells (ChIP-seq)

Project description:Knowledge of both the global chromatin structure and the gene expression programs of human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells should provide a robust means to assess whether the genomes of these cells have similar pluripotent states. Recent studies have suggested that ES and iPS cells represent different pluripotent states with substantially different gene expression profiles. We describe here a comparison of global chromatin structure and gene expression data for a panel of human ES and iPS cells. Genome-wide maps of nucleosomes with histone H3K4me3 and H3K27me3 modifications indicate that there is little difference between ES and iPS cells with respect to these marks. Gene expression profiles confirm that the transcriptional programs of ES and iPS cells show very few consistent differences. Although some variation in chromatin structure and gene expression was observed in these cell lines, these variations did not serve to distinguish ES from iPS cells. Examination of two histone modifications (H3K4me3 and H3K27me3) in 6 human ES cell lines, 8 human iPS cell lines, and 1 fibroblast cell line.

2010-08-09 | E-GEOD-23455 | biostudies-arrayexpress

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells (ChIP-seq)

2010-08-09 | GSE23455 | GEO

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells (Affymetrix)

2010-08-09 | GSE23402 | GEO

Reprogramming human somatic cells to a pluripotent state

Project description:Here we compare the global gene expression of induced pluripotent stem cell (iPS) cells with those of normal human embryonic stem cells and parental mesenchymal cells. Keywords: reprogramming, iPS We used 1 chip/sample (3 iPS clones for each mesenchymal clone - 12 iPS clones; 4 mesenchymal clones and 5 normal human ES cell lines).

2010-05-27 | E-GEOD-9071 | biostudies-arrayexpress

Inducible iPS Cells Support Full-term Development of Tetraploid BlastocystâComplemented Embryos

Project description:Differentiated somatic cells can be reprogrammed into induced pluripotent stem (iPS) cells by forced expression of four transcription factorsâOct4, Sox2, Klf4, and c-Myc. However, it remains undetermined whether the reprogrammed iPS cells are fully pluripotent, resembling normal embryonic stem (ES) cells, given that no iPS cell lines have been shown to possess the capability to autonomously generate full-term mice after injection into tetraploid blastocysts. Here, we provide evidence demonstrating that iPS cells induced by the four transcription factors can be fully pluripotent and that full-term mice can be produced from complemented tetraploid blastocysts. This work serves as a proof of principle that iPS cells can generate full term embryos by tetraploid complementation. We compared the gene expression profile of iPS cell, ES cell and MEF. ES cell and MEF served as control for iPS cell. Three biological repeats were included for each line.

2010-08-18 | E-GEOD-17004 | biostudies-arrayexpress

Expression data from undifferentiated and iPS cells differentiated to a myogenic fate [hPAX7]

Project description:Here, we report the generation of human induced Pluripotent Stem (iPS) cell reporter line in which a venus fluorescent protein have been introduced into the PAX7 locus. We use microarrays to compare the transcriptome of PAX7-venus+ cells after 3 weeks of myogenic differentiation to that of undifferentiated iPS Satellite cells (SC) are muscle stem cells which can regenerate adult muscles upon injury. Most SC originate from PAX7-positive myogenic precursors set aside during development. While myogenesis has been studied in mouse and chicken embryos, little is known about human muscle development. Here, we use microarrays to compare the transcriptome of myogenic cells differentiated in vitro from human and mouse ES and iPS cells reporter cell lines. We generated fluorescent reporter lines in which a fluorescent protein was introduced into the loci coding for Pax7 (mouse ES and human iPS) or MYOG (human iPS). Mouse ES and human iPS cells were differentiated to the myogenic lineage in vitro for three weeks according to the protocols described in Chal et al, Nature Biotech 2015 and to Chal, Al Tanoury et al, Nature Protocols, 2016. Fluorescent Pax7 or MYOG-positive cells were FACS-sorted after 3-weeks of differentiation in vitro and we used Affymetrix microarrays to analyze the transcriptome of the purified mouse and human cell populations and compare it to the transcriptome of undifferentiated mouse ES or human iPS cells.

2020-04-22 | GSE149055 | GEO

Expression data from undifferentiated and iPS cells differentiated to a myogenic fate [MYOG]

Project description:Here, we report the generation of human induced Pluripotent Stem (iPS) cell reporter line in which a venus fluorescent protein have been introduced into the MYOGENIN (MYOG) locus. We use microarrays to compare the transcriptome of MYOG-venus+ cells after 3 weeks of myogenic differentiation to that of undifferentiated iPS Satellite cells (SC) are muscle stem cells which can regenerate adult muscles upon injury. Most SC originate from PAX7-positive myogenic precursors set aside during development. While myogenesis has been studied in mouse and chicken embryos, little is known about human muscle development. Here, we use microarrays to compare the transcriptome of myogenic cells differentiated in vitro from human and mouse ES and iPS cells reporter cell lines. We generated fluorescent reporter lines in which a fluorescent protein was introduced into the loci coding for Pax7 (mouse ES and human iPS) or MYOG (human iPS). Mouse ES and human iPS cells were differentiated to the myogenic lineage in vitro for three weeks according to the protocols described in Chal et al, Nature Biotech 2015 and to Chal, Al Tanoury et al, Nature Protocols, 2016. Fluorescent Pax7 or MYOG-positive cells were FACS-sorted after 3-weeks of differentiation in vitro and we used Affymetrix microarrays to analyze the transcriptome of the purified mouse and human cell populations and compare it to the transcriptome of undifferentiated mouse ES or human iPS cells.

2020-04-21 | GSE148994 | GEO

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