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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Investigation of Isogenic Human Embryonic Stem Cells and Derived Induced Pluripotent Stem Cells and Differentiated Line

ABSTRACT: Briefly, the well characterized female hES cell line H9 was allowed to differentiate into a clonally purified mortal splanchnopleuric mesodermal somatic cell line EN13. The EN13 line was subsequently virally reprogrammed back to an induced pluripotent state (we term re-H9) using OCT4, SOX2, KLF4 retroviral vectors creating isogenic lines of hESC, hiPSC and mortal cells. Our results reveal several important differences between embryo-derived H9 and the induced re-H9 stem cells. We find a dysregulation of genes involved in imprinting and altered expression of X-chromosome localized genes in re-H9 cells. 10 Samples. 1 hESC line, 6 isogenic hiPSC lines, 1 non-isogenic hiPSC line, 1 isogenic mortal line, 1 non-isogenic mortal line

ORGANISM(S): Homo sapiens

SUBMITTER: Jonathan Teichroeb

PROVIDER: E-GEOD-31845 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Investigation of Isogenic Human Embryonic Stem Cells and Derived Induced Pluripotent Stem Cells and Differentiated Line

Project description:Briefly, the well characterized female hES cell line H9 was allowed to differentiate into a clonally purified mortal splanchnopleuric mesodermal somatic cell line EN13. The EN13 line was subsequently virally reprogrammed back to an induced pluripotent state (we term re-H9) using OCT4, SOX2, KLF4 retroviral vectors creating isogenic lines of hESC, hiPSC and mortal cells. Our results reveal several important differences between embryo-derived H9 and the induced re-H9 stem cells. We find a dysregulation of genes involved in imprinting and altered expression of X-chromosome localized genes in re-H9 cells.

2011-09-03 | GSE31845 | GEO

Establishing a molecular phenotype for Angelman Syndrome stem cell-derived neurons

Project description:mRNAseq on (1) isogenic control and Angelman Syndrome pluripotent stem cell-derived neurons or (2) antisense oligonucleotide-treated H9 hESC-derived neurons

2021-04-01 | GSE160747 | GEO

Analysis of the protein cargo of extracellular vesicles isolated from cultured line H9 human stem cells

Project description:Extracellular vesicles (EV) are secreted by nearly every mammalian cell type and contain a wealth of bioactive cargo capable of modulating target cell physiology and function though a variety of paracrine signaling mechanisms (Leavitt et al., 2019). Human embryonic stem cell (hESC)-derived extracellular vesicles (hESC-derived EV), were extracted from the hESC line H9 (WA09 Wicell Research Institute, Inc., Madison, WI). We analyzed the bioactive protein cargo to identify components that help to resolve radiation-induced injury to the lung in mice when injected in vivo.

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Homo sapiens strain:H9 hESC line

Project description:Homo sapiens strain:H9 hESC line Exome

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Comparative genomic hybridization of hiPSC stem cell lines.

Project description:The Purpose of this series of experiments is to identify copy number variations, duplications, and deletions in human induced pluripotent stem (hiPSC) cell lines. Genomic DNA of different human induced pluripotent stem cell lines are extracted and hybridized to NimbleGen CGH microarray, using genomic DNA of hESC H1 or H9 as common reference. Difference between different stem cell lines will be revealed.

2012-01-07 | E-GEOD-33484 | biostudies-arrayexpress

Genome-wide transcriptomic analysis of cardiomyocyte differentiation from human embryonic stem cells and iPS cells (RNA-seq)

Project description:In this study, time-course transcriptome profiling of caidiomyocyte differentiation derived from human hESCs and hiPSCs was investigated. Two hiPSC lines (C15 and C20) and two hESC lines (H1 and H9) were differentiated to caidiomyocytes. The cells were collected for RNA-seq analysis at day0(undifferentiated cells) day2 (mesoderm), day4 (cardiac mesoderm) and day30 (cardiomyocytes) using Illumina HiSeq 2000 sequencer.

2017-07-10 | GSE85331 | GEO

Genome-wide chromatin accessibility profiling of cardiomyocyte differentiation from human embryonic stem cells and iPS cells (ATAC-seq)

Project description:In this study, time-course genome-wide chromatin accessibility of caidiomyocyte differentiation derived from human hESCs and hiPSCs was profiled. Two hiPSC lines (C15 and C20) and two hESC lines (H1 and H9) were differentiated to caidiomyocytes by ATAC-seq. The cells were collected for ATAC-seq at day 0(undifferentiated cells) day 2 (mesoderm), day 4 (cardiac mesoderm) and day 30 (cardiomyocytes).

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Characterization of Definitive Endoderm formation from HESC and iPSC lines by Microarray analysis

Project description:HESC-H9 and iPSC lines 3.5, 3.6 and 3.12 were analyzed using Affymetrix microarray before and after Definitive Endoderm (DE) formation. DE was induced using the ActivinA differentiation protocol described by D'Amour et al., 2006 (PMID: 16258519) Clustering analysis of transcripts that were differentially regulated during DE formation indicated that iPSC lines 3.5 and 3.12 differentiate in manner that is highly similar to HESC-H9 cells iPSC line 3.6 had a more divergent transcriptional profile.

2010-12-25 | GSE25557 | GEO

Gene expression profile of hESC/hIPC-derived keratinocytes

Project description:To induce the differentiation, undifferentiated human pluripotent stem cells (both hESC andh iPSC; T0 time point) were transferred into 20% O2 atmosphere environment and treated with mTESR1 basal media supplemented with 1 μM ATRA (Sigma-Aldrich) and 25 ng/ml BMP4 (R&D) for 7 days (Induction). To select for the cells that acquired early ectodermal fate, cells were harvested and re-plated onto freshly prepared 3D human dermal fibroblast ECM at a density of 5-10x10^3 cells per cm2 and grown in DMEM:Ham F12 (3:1) (Life Technologies) supplemented with 1 μM ATRA and 25 ng/ml BMP4 for a further 7 days (Selection). To enrich for putative epidermal progenitors, rapid-adhesion to type IV collagen-coated dishes was used, and the rapidly-adhering cells were cultured in DK SFM supplemented with 1 μM ATRA for 7 days (Enrichment). After that, the cells were cultured in EpiLife medium (Life Technologies) for a further 7 days (Expansion) before final harvest (T3 time point) and analysis. We analyzed here gene expression profiles of undifferentiated hESC/hiPSC (T0), hESC/hIPC-derived keratinocytes (T3) and primary normal human keratinocytes from skin biopsy (NHK). We found that hESC/hIPC-derived keratinocytes are similar to NHK. Biological triplicates of undifferentiated (T0) hESC (KCL034) and hiPSC lines (iKCL004, iKCL011) were compared with hESC/hiPSC-derived keratinocytes (T3), primary human keratinocyes (NHK) and fibroblasts (BJ).

2015-04-01 | E-GEOD-55898 | biostudies-arrayexpress

Transcriptome analysis of pancreatic progenitors differentiated from H9 human embryonic stem cells and induced pluripotent stem cells derived from a Mitchell-Riley Syndrome patient

Project description:Skin biopsies were obtained from a patient with Mitchell-Riley syndrome caused by a homozygous frame-shift mutation (c.1129C>T) in the RFX6 gene that leads to a premature stop codon (p.Arg377X). The patient suffered severe pancreatic agenesis, in common with other Mitchell-Riley syndrome patients. Fibroblasts from the biopsy were reprogrammed to generate a human induced pluripotent stem cell (hiPSC) line (MRS2-6). To assess the effects of the mutant RFX6 allele on pancreas formation and identify direct targets of the transcription factor RFX6, MRS2-6 and H9 control human embryonic stem cells (hESC) were differentiated into pancreatic progenitors. Samples were harvested for RNA isolation and whole transcriptome analysis at days 4 (definitive endoderm), 7 and 8 (gut tube), and 12 (pancreatic progenitors).

2020-03-30 | E-MTAB-6626 | biostudies-arrayexpress

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