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Single cell RNA-seq analysis of feeder-free iPSC-derived gliogenic NS/PCs and neurogenic NS/PCs

ABSTRACT: We performed single cell RNA sequencing to analyze the transcriptional profile of gliogenic NS/PCs and neurogenic NS/PCs derived from the same parental feeder-free iPSCs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE138302 | GEO | 2020/12/09

REPOSITORIES: GEO

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Single cell RNA-seq analysis of feeder-free iPSC-derived gliogenic NS/PCs and neurogenic NS/PCs

Project description:Single cell RNA-seq analysis of feeder-free iPSC-derived gliogenic NS/PCs and neurogenic NS/PCs

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Sequential expression profile of feeder-free iPSC-derived gliogenic NS/PCs by RNA-seq

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Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of neural stem/progenitor cells (NS/PCs) in control and prenatal valproic acid (VPA) exposed mice with or without voluntary exercise

Project description:Purpose: The goals of this study are to investigate the effect of prenatal VPA exposure on transcriptome profile of NS/PCs during development, and the effect of exercise on transcriptome profile of adult NS/PCs in prenatal VPA exposed mice. Methods: NS/PCs mRNA profiles of embryonic day15 (E15), postnatal day5 (P5) and 12-week-old (12w) contol mice and E15, P5, 12w with or without voluntary exercise prenatal VPA exposed mice were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with a method: TopHat/Bowtie2 followed by Cufflinks.NS/PCs were isolated from forebrain (E15), hippocampal dentate gyrus (P5 and 12w) of Nestin-EGFP mice. Results: Hierarchial clustering using eighteen samples (E15 Ctrl, E15 VPA, P5 Ctrl, P5 VPA, 12w Ctrl, 12w VPA, three samples each) identified three distinct clusters composed of NS/PCs derived from each developmental stage. Gene set enrichment analysis using transcriptome of E15 Ctrl and E15 VPA revealed a significant increase in the expression of neuron differentiation- and nervous system development-related genes in VPA compared with Ctrl. Gene ontology analysis of biological processes using differentially expressed genesin 12w VPA compared with 12w Ctrl revealed that expression levels of cell-migration-associated genes were altered. Voluntary running mostly amended both positively and negativly distorted gene expression in the 12w VPA compared with 12w Ctrl NS/PCs. The altered expression of cell migration-related genes was largely normalized by voluntary running.

2018-03-15 | GSE101239 | GEO

Single cell study of neural stem cells derived from human iPSCs reveal distinct progenitor populations with neurogenic and gliogenic potential (1)

Project description:Single cell RNA-seq study of induced pluripotent stem cell derived neural stem cells. Analysis of gene expression over cell clusters identified inherent presence of neurogenic progenitors and gliogenic progenitors in established neural stem cells. This study aids to explain heterogeneity of neural stem cell identity and resolves gene expression enrichment in subpopulations of diverse progenitors. Processed and quality controlled data sets used for generating figure 4 in published article. Single cell raw data files for experiments were not made available.

2019-10-24 | E-MTAB-8363 | biostudies-arrayexpress

Single cell study of neural stem cells derived from human iPSCs reveal distinct progenitor populations with neurogenic and gliogenic potential (2)

Project description:Single cell RNA-seq study of induced pluripotent stem cell derived neural stem cells. Analysis of gene expression over cell clusters identified inherent presence of neurogenic progenitors and gliogenic progenitors in established neural stem cells. This study aids to explain heterogeneity of neural stem cell identity and resolves gene expression enrichment in subpopulations of diverse progenitors. Processed and quality controlled data sets used for generating figure 2 in published article. Single cell raw data files for experiments are not available for public download.

2019-10-24 | E-MTAB-8379 | biostudies-arrayexpress

Single cell study of neural stem cells derived from human iPSCs reveal distinct progenitor populations with neurogenic and gliogenic potential (3)

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2019-10-24 | E-MTAB-8383 | biostudies-arrayexpress

Identification of Nfia-target genes in mid-gestational NS/PCs

Project description:Identification of Nfia-target genes in mid-gestational NS/PCs

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Project description:The purpose of this study is to identify Nfia-target genes, and then clarify how Nifa induces gliogenic potential during brain development.

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Analysis of Mll1-deficiency identifies neurogenic transcriptional modules and Brn4 as a factor for direct astrocyte-to-neuron reprogramming

Project description:BACKGROUND: Mixed lineage leukemia-1 (Mll1) epigenetically regulates gene expression patterns that specify cellular identity in both embryonic development and adult stem cell populations. In the adult mouse brain, multipotent neural stem cells (NSCs) in the subventricular zone (SVZ) generate new neurons throughout life and Mll1 is required for this postnatal neurogenesis but not for glial cell differentiation. Analysis of Mll1-dependent transcription may identify neurogenic genes useful for the direct reprogramming of astrocytes into neurons. OBJECTIVE: To identify Mll1-dependent transcriptional modules and determine whether genes in the neurogenic modules can be used to directly reprogram astrocytes into neurons. METHODS: We performed gene coexpression module analysis on microarray data from differentiating wild-type and Mll1-deleted SVZ NSCs. Key developmental regulators belonging to the neurogenic modules were overexpressed in Mll1-deleted cells and cultured cortical astrocytes, and cell phenotypes were analyzed by immunocytochemistry and electrophysiology. RESULTS: Transcriptional modules that correspond to neurogenesis were identified in wild-type NSCs. Modules related to astrocytes and oligodendrocytes were enriched in Mll1-deleted NSCs, consistent with their gliogenic potential. Overexpression of genes selected from the neurogenic modules enhanced the production of neurons from Mll1- deleted cells, and the overexpression of Brn4 (Pou3f4) in non-neurogenic cortical astroglia induced their transdifferentiation into electrophysiologically active neurons. CONCLUSIONS: Our results demonstrate that Mll1 is required for the expression of neurogenic - but not gliogenic - transcriptional modules in a multipotent NSC population and further indicate that specific Mll1-dependent genes may be useful for direct reprogramming strategies.

2016-03-06 | GSE56835 | GEO

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