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Transcriptome analysis of single cell-derived hiPSC-lt-NES cell clones

ABSTRACT: To identify cell-populations within human iPSC-derived long-term self-renewing neural epithelial stem cells (hiPSC-lt-NES cells) which retain capacities to generate undesired grafts, we established single cell-derived hiPSC-lt-NES cell clones and performed gene expression microarray analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE166051 | GEO | 2023/06/04

REPOSITORIES: GEO

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Transcriptome analysis of hiPSC derived lt-NES cells

Project description:To identify cell-populations within human iPSC-derived long-term self-renewing neural epithelial stem cells (hiPSC-lt-NES cells) which retain capacities to generate undesired grafts, we performed gene expression microarray analysis.

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Single Cell Transcriptomic Analysis of hiPSC-lt-NES cells

Project description:We performed single-cell RNA-seq of human iPSC-derived long-term self-renewing neural epithelial stem cells (hiPSC-lt-NES cells) using Quartz-seq methods to characterize cellular heterogeneity .

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Analysis of gene expression profile in the control and CHD7-knockdown hiPSC-derived lt-NES cells (scRNA-Seq)

Project description:CHARGE syndrome is a congenital disorder caused by mutations in Chromodomain Helicase DNA-binding domain 7 (CHD7) gene. We performed single cell RNA-seq analysis in CTRL and CHD7-knockdown lt-NES cells.

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Analysis of gene expression profile in the control and CHD7-knockdown hiPSC-derived lt-NES cells (scRNA-Seq)

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Project description:We performed a microarray experiment to analyze the transcriptional profile of human fetal tissue derived neural stem/progenitor cells, human iPSCs, or human iPSC-derived neural stem/progenitor cells generated using xenogenic or xeno-free reagents. Gene expression patterns were compared among human fetal tissue derived neural stem/progenitor cells, human iPSCs, or human iPSC-derived neural stem/progenitor cells generated using xenogenic or xeno-free reagents. Samples with a title including "Xf" (201B7-lt-NES (Xf)-1, 201B7-lt-NES (Xf)-2, 1210B2-lt-NES (Xf)-1,1210B2-lt-NES (Xf)-2, 1231A3-lt-NES (Xf)-1, 1231A3-lt-NES (Xf)-2) correspond to human iPSC-derived neural stem/progenitor cells generated using xeno-free reagents, whereas samples with a title including "Con" (201B7-lt-NES (Con)-1, 201B7-lt-NES (Con)-2) correspond to those generated using xenogenic reagents.

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Global Transcriptional analysis of human spinal cord and neocortical neuroepithelial stem (NES) cells

Project description:We report the transcriptional profile of human spinal cord and neocortical neuroepithelial stem cells (SC-NES and NCX-NES cells) to identify potential engraftment markers in the lesioned spinal cord. We report that cells with a homologous neuroanatomical origin robustly integrate in the host tissue compared to cells with a different regional identity. Specifically, we describe that SC-NES cells display elective integration properties in the lesioned spinal cord compared to NCX-NES cells and that these properties are due to a combination of intrinsic and extrinsic factors. Upon transplantation, SC-NES cells differentiate into neurons and glial cells and extend lond-distance axons, whereas NCX-NES cells remain undifferentiated and display poor integration properties. SC-NES cell upregulate genes related to neurogenesis. In particular. we emphasize the upregulation of MTURN (maturin), ATCAY, PTN (pleiotropin), KAL1 (anosmin), SYT4 and SYT13.

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Cellular proteomic profiling using proximity labelling by TurboID-NES in microglial and neuronal cell lines.

Project description:Different brain cell types play distinct roles in brain development and disease via cellular mechanisms. Molecular characterization of these cellular mechanisms using cell type-specific approaches, particularly at the protein (proteomic) level, can provide biological and therapeutic insights. Conventional approaches to investigate cell type-specific proteomes from brain pose several technical barriers. To overcome these, in vivo proteomic labeling with proximity dependent biotinylation of cytosolic proteins using TurboID with a Nuclear Export Sequence (TurboID-NES), coupled with mass spectrometry (MS) of labeled proteins, has emerged as a powerful strategy to sample cell type-specific proteomes in the native state of cells without need for cellular isolation. To complement in vivo proximity labeling approaches, in vitro studies are needed to ensure that cellular proteomes using the TurboID-NES approach are representative of the whole cell proteome, and capture cellular responses to stimuli without disruption of cellular processes. We generated murine neuroblastoma (N2A) and microglial (BV2) lines stably expressing TurboID-NES to biotinylate the cellular proteome for downstream purification and analysis using MS. TurboID-NES expression and biotinylation did not significantly impact homeostatic cellular proteomes of BV2 and N2A cells, and did not affect cytokine production or mitochondrial respiration of BV2 cells under resting or lipopolysaccharide (LPS)-stimulated conditions. TurboID-NES mediated biotinylation captured 59% of BV2 and 65% of N2A proteomes under resting conditions. Acute LPS treatment significantly altered microglial proteomes, but not N2A proteomes, and the LPS effect was partly captured by analysis of the TurboID-NES-labeled proteome of BV2 cells.

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Investigating hiPSC-CMs_DongLi

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Expression data from p53 knocked-down human neuroepithelial stem (NES) cells

Project description:In this study, we take advantage of human induced pluripotent stem (iPS) cell-derived neural stem cells to study the role of p53 during human brain development. We knocked down (KD) p53 in human neuroepithelial stem (NES) cells derived from iPS cells. Upon p53KD, NES cells rapidly show centrosome amplification and genomic instability. Gene expression analysis show downregulation of genes involved in oxidative phosphorylation (OXPHOS) upon loss of p53. In addition, p53KD neural stem cells upregulate genes involved in neuronal differentiation and display an increased pace of differentiating into neurons and exhibit a phenotype corresponding to more mature neurons compared to control neurons. Taken together, this demonstrates an important role for p53 in controlling genomic stability of neural stem cells and regulation of neuronal differentiation. We used microarrays to identify gene expression changes in human NES cells upon p53 knockdown

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