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Transcriptomic profile of human induced pluripotent stem cells at single cell resolution.

ABSTRACT: Transcriptomic profile of human induced pluripotent stem cells at single cell resolution.

PROVIDER: PRJEB32421 | ENA |

REPOSITORIES: ENA

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Transcriptomic profile of human induced pluripotent stem cells at single cell resolution.

Project description:We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlexTM and TeSRTM-E8TM media. Single-cell transcriptome sequencing was performed for 20,962 cells from two cell lines grown in the two media. Analysis of transcriptomic profile revealed similar expression of core pluripotency genes, as well as genes associated with naive and primed states of pluripotency. Single cell analysis of the four samples revealed a shared subpopulation structure with three main subpopulations different in pluripotency states. By implementing a machine learning approach, we estimated that 60-96% of the cells in the ground/naive subpopulations and 98-99% of the cells in the primed subpopulations are similar between all four samples. The single cell RNA sequencing analysis of iPSC lines grown in both media is the first report of the molecular pathways modulated in StemFlex medium and how they compare to those modulated in TeSR-E8 medium.

2019-05-08 | E-MTAB-6524 | biostudies-arrayexpress

The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells

Project description:Assessing relevant molecular differences between human-induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs) is important, given that such differences may impact their potential therapeutic use. Controversy surrounds recent gene expression studies comparing hiPSCs and hESCs. Here, we present an in-depth quantitative mass spectrometry-based analysis of hESCs, two different hiPSCs and their precursor fibroblast cell lines. Our comparisons confirmed the high similarity of hESCs and hiPSCS at the proteome level as 97.8% of the proteins were found unchanged. Nevertheless, a small group of 58 proteins, mainly related to metabolism, antigen processing and cell adhesion, was found significantly differentially expressed between hiPSCs and hESCs. A comparison of the regulated proteins with previously published transcriptomic studies showed a low overlap, highlighting the emerging notion that differences between both pluripotent cell lines rather reflect experimental conditions than a recurrent molecular signature. See the Data Processing section of the published paper concerning the bioinformatics pipeline used. PMCID: PMC3261715 PMID: 22108792 Mol Syst Biol. 2011 Nov 22;7:550. doi: 10.1038/msb.2011.84. The quantitative proteomes of human-induced pluripotent stem cells and embryonic stem cells. Munoz J, Low TY, Kok YJ, Chin A, Frese CK, Ding V, Choo A, Heck AJ. Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.

2013-02-01 | PXD000134 | Pride

Genome-wide analysis of the gene expression profile of in vivo induced pluripotent stem cells

Project description:Analysis of the gene expression profile of a novel type of pluripotent stem cells (in vivo induced pluripotent stem cells, named i2PS cells) obtained by reprogramming BALB/c mice hepatocytes in vivo. The hypothesis tested in the present study is that in vivo induced pluripotent stem cells will have a similar gene expression profile to that of other pluripotent stem cells. Hence the embryonic stem cell line E14TG2A is used as a reference in this study. Results provide valuable information for the overall molecular characterisation of cells that have been reprogrammed to pluripotency in vivo, together with the confirmation of their pluripotent character at the gene expression level.

2014-03-19 | GSE55996 | GEO

Genome-wide analysis of the gene expression profile of in vivo induced pluripotent stem cells

2014-03-19 | E-GEOD-55996 | biostudies-arrayexpress

Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells

Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis

2013-01-16 | ST000003 | MetabolomicsWorkbench

Metabolomics Workbench ST000003 - GNPS - Metabolomic analysis of mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells

Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis

2018-08-02 | MSV000082680 | GNPS

Whole-Genome Methylation Profile of Fibroblast-Derived Isogenic Induced Pluripotent Stem Cells

Project description:Whole-Genome Methylation Profile of Fibroblast-Derived Isogenic Induced Pluripotent Stem Cells

| PRJNA414786 | ENA

Temporal single-cell transcriptomic profiling of cardiac differentiation in human induced pluripotent stem cells with NOTCH1 mutations

Project description:Pathological variants in NOTCH1 have been implicated in multiple types of congenital heart defects including bicuspid aortic valve and hypoplastic left heart syndrome (HLHS). To probe how NOTCH1 deficiency affects cardiac development, we generated homozygous NOTCH1 knockout (N1KO) human induced pluripotent stem cells (iPSCs). We then ran single-cell RNA-seq to temporally profile transcriptomic changes during cardiac differentiation in wild type (WT) and N1KO iPSCs. We collected differentiating cells at multiple time points corresponding to different development stages, i.e., Day 0 (D0: pluripotent stem cell), D2 (mesoderm), D5 (cardiac mesoderm), D10 (cardiac progenitor), D14 (early cardiomyocyte), and D30 (fetal cardiomyocyte). Single-cell transcriptomics analysis reveals that NOTCH1 disruption impairs human ventricular cardiomyocyte differentiation and proliferation through balancing cell fate determination of cardiac mesoderm toward the first heart field, second heart field, and epicardial lineages.

2022-12-21 | GSE196632 | GEO

Human induced pluripotent stem cell differentiation to cardiomyocytes

Project description:Shotgun proteomics analysis of directed differentiation of human induced pluripotent stem cells to cardiomyocytes

2019-12-16 | PXD013426 | Pride

Hyperosmolarity stress associated proteomic changes in induced pluripotent stem cells.

Project description:Comparison of hyperosmolarity stress associated proteomic changes between induced pluripotent stem cells (hiPSCs/IMR90-01) and differentiated SH-SY5Y cells.

2020-10-23 | MSV000086363 | MassIVE

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