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Comparison of hiPSCs, hESCs and fibroblasts

ABSTRACT: In our study, PRDM14 and NFRkB were found to enhance the reprogramming of human fibroblasts to hiPSCs in the presence of OCT4, SOX2, KLF4, with/without c-MYC (OSK/OSKC). To examnie if the obtained hiPSC share similar expression signature with hESC, we conducted the microarray analysis on the hiPSCs, hESCs and fibroblasts. The result showed that all of the examined hiPSCs resembled hESCs, but differed from fibroblasts MRC5. 4 hiPSC lines, 2 hESC lines and 1 type of fibroblasts were analyzed in total. Each sample is done in duplicates.

ORGANISM(S): Homo sapiens

SUBMITTER: NA-YU CHIA

PROVIDER: E-GEOD-22792 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity.

Chia Na-Yu NY Chan Yun-Shen YS Feng Bo B Lu Xinyi X Orlov Yuriy L YL Moreau Dimitri D Kumar Pankaj P Yang Lin L Jiang Jianming J Lau Mei-Sheng MS Huss Mikael M Soh Boon-Seng BS Kraus Petra P Li Pin P Lufkin Thomas T Lim Bing B Clarke Neil D ND Bard Frederic F Ng Huck-Hui HH

Nature 20101017 7321

The derivation of human ES cells (hESCs) from human blastocysts represents one of the milestones in stem cell biology. The full potential of hESCs in research and clinical applications requires a detailed understanding of the genetic network that governs the unique properties of hESCs. Here, we report a genome-wide RNA interference screen to identify genes which regulate self-renewal and pluripotency properties in hESCs. Interestingly, functionally distinct complexes involved in transcriptional ...[more]

PMID: 20953172

Similar Datasets

Comparison of hiPSCs, hESCs and fibroblasts

Project description:In our study, PRDM14 and NFRkB were found to enhance the reprogramming of human fibroblasts to hiPSCs in the presence of OCT4, SOX2, KLF4, with/without c-MYC (OSK/OSKC). To examnie if the obtained hiPSC share similar expression signature with hESC, we conducted the microarray analysis on the hiPSCs, hESCs and fibroblasts. The result showed that all of the examined hiPSCs resembled hESCs, but differed from fibroblasts MRC5.

2010-10-20 | GSE22792 | GEO

Comparison of DNA methylation profilings between hESCs and hiPSCs

Project description:It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine. Bisulphite converted DNA from 10 hESCs, 49 hiPSCs, 2 hECCs, 6 somatic cells and 3 cancer cell lines were hybridized to the Illumina Infinium 27k Human Methylation Beadchip.

2013-12-03 | E-GEOD-42448 | biostudies-arrayexpress

Comparison of miRNA expression profilings between hESCs and hiPSCs

Project description:It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine. We extracted total RNA from 10 hESCs, 49 hiPSCs, 2 hECCs, 6 somatic cells and 3 cancer cell lines and hybridized them to Agilent miRNA expression microarrays.

2013-12-03 | E-GEOD-42446 | biostudies-arrayexpress

Comparison of gene expression profilings between hESCs and hiPSCs

Project description:It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine. We extracted total RNA from 10 hESCs, 49 hiPSCs, 2 hECCs, 6 somatic cells and 3 cancer cell lines and hybridized them to Agilent gene expression microarrays.

2013-12-03 | E-GEOD-42445 | biostudies-arrayexpress

Comparison of gene expression profilings between hESCs and hiPSCs

2013-12-03 | GSE42445 | GEO

Comparison of DNA methylation profilings between hESCs and hiPSCs

2013-12-03 | GSE42448 | GEO

Comparison of miRNA expression profilings between hESCs and hiPSCs

2013-12-03 | GSE42446 | GEO

Expression data from hESCs, hiPSCs and human fibroblasts.

Project description:Detailed analysis comparing hiPSC lines that were newly generated and compared them to already established hiPSC lines We used microarrays to detail various hiPSC lines to confirm faithful reprogramming. hESCs, hiPSCs and human fibroblasts for RNA extraction and hybridization on Affymetrix arrays.

2010-08-06 | E-GEOD-22392 | biostudies-arrayexpress

Comparison of gene expression profilings between SFEBq differentiation-defective clones and good clones

Project description:It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine. We extracted total RNA from 10 hESCs and 40 hiPSCs, and hybridized them to Agilent gene expression microarrays.

2013-12-03 | E-GEOD-42452 | biostudies-arrayexpress

Affymetrix SNP6.0 data for human induced pluripotent stem cells (hiPSCs), human Fibroblasts, and human embryonic stem cells (hESCs)

Project description:In this study, copy number variations of hiPSCs were compared to their parental fibroblast lines and hESCs to assess the level of DNA damage incurred due to the process of reprogramming of somatic cells. Higher levels of copy number changes were observed in hiPSCs (especially in early passage hiPSCs) compared to the other cell types. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from in vitro cultured cells. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 35 hiPSC samples, 2 hESC samples, and 5 fibroblast samples. Other hESC and the reference Hapmap sample CEL files were obtained from Narva et al. 2010, Nat. Biotech., GEO accession code GSE15097 (see readme file below for details).

2011-01-31 | E-GEOD-26173 | biostudies-arrayexpress

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