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Chromatin and gene-regulatory dynamics of mouse nephron progenitors at single-cell resolution [Single cell Multiome ATAC + Gene Expression]

ABSTRACT: Chromatin and gene-regulatory dynamics of mouse nephron progenitors at single-cell resolution [Single cell Multiome ATAC + Gene Expression]

PROVIDER: PRJNA750048 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15258019_1.fastq.gz	Fastqsanger.gz
	SRR15258019_2.fastq.gz	Fastqsanger.gz
	SRR15258020_1.fastq.gz	Fastqsanger.gz
	SRR15258020_2.fastq.gz	Fastqsanger.gz
	SRR15258021_1.fastq.gz	Fastqsanger.gz

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Chromatin and gene-regulatory dynamics of mouse nephron progenitors at single-cell resolution [Single cell Multiome ATAC + Gene Expression]

Project description:Background: Unraveling the dynamic accessibility of regulatory chromatin at single-cell resolution is key to understanding stem/progenitor cell fate choices in health and disease. Nephron progenitor cells (NPCs) are a multipotent population giving rise to all cell types of the nephron, from the glomerular epithelium to the distal tubule. At any given time, the NPC’s choice to self-renew or differentiate and gain a new identity is determined not only by its transcription factor repertoire but also by the genome accessibility of the cognate cis-regulatory elements. Methods: We performed singleome and multiome analysis of chromatin accessibility and gene expression in thousands of embryonic and neonatal NPCs toward defining the regulatory landscape driving fate choices during nephrogenesis. Results: We show that chromatin accessibility recovers the diverse states of NPCs and precursor states of proximal and distal nephron epithelial cells. We define the key cell type-specific transcriptional regulators across pseudotime and NPC age. We find that chromatin accessibility in the podocyte lineage is established early in the trajectory and identify a subset of Forkhead factors exhibiting high chromatin activity in podocyte precursors. We also determined that strong linkages between cis-regulatory elements and expression levels distinguish fate-determining TFs. Conclusions: Single-cell mapping of accessible and active chromatin defines the regulatory landscape of nephrogenesis and provides a foundation for future studies in disease states characterized by abnormal nephrogenesis.

2022-04-01 | GSE180900 | GEO

Chromatin and gene-regulatory dynamics of mouse nephron progenitors at single-cell resolution [scATAC-Seq]

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Project description:we used single-cell multiome analysis to profile the transcriptome and epigenome of MSCs from four healthy donors.

2023-11-09 | GSE228669 | GEO

Single-cell chromatin and gene-regulatory dynamics of mouse nephron progenitors [ChIP-seq]

Project description:Background: We reasoned that unraveling the dynamic changes in accessibility of genomic regulatory elements and gene expression at single-cell resolution will inform the basic mechanisms of nephrogenesis. Methods: We performed single-cell ATAC-seq and RNA-seq both individually (Singleomes; Six2GFP cells) and jointly in the same cells (Multiomes; kidneys) to generate integrated chromatin and transcriptional maps in mouse embryonic and neonatal nephron progenitor cells (NPCs). Results: We demonstrate that singleomes and multiomes are comparable in assigning most cell states, identification of new cell type markers, and defining the transcription factors driving cell identity. However, multiomes are more precise in defining the progenitor population. Multiomes identified a “pioneer” bHLH/Fox motif signature in NPCs. Moreover, we identified a subset of Fox factors exhibiting high chromatin activity in podocytes. One of these Fox factors, Foxp1, is important for nephrogenesis. Key nephrogenic factors are distinguished by strong correlation between linked gene-regulatory elements and gene expression. Conclusion: Mapping the regulatory landscape at single-cell resolution informs the regulatory hierarchy of nephrogenesis. Paired single-cell epigenomes and transcriptomes of nephron progenitors should provide a foundation to understand prenatal programming, regeneration following injury, and ex vivo nephrogenesis.

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Intrinsic age-dependent changes and cell-cell contacts regulate nephron progenitor lifespan

Project description:Purpose: To use single-cell RNA-Seq analysis of nephron progenitors in order to determine transcrptional differences as nephron progenitors age. Methods: Using a combination of FACS sorting and a Fluidigm Single-cell auto-prep system, we generated high-throughput RNA-SEQ data of nephron progenitors during development Results: Single cells transcriptome profiling of nephron progenitors revealed progressive age-dependent changes with heterogeneity increasing in older populations. 96-single cell transcriptomes were determined from nephron progenitors of e14.5, e18.5 and P0 using Cited1GFP transgenic animals

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Single-cell chromatin and gene-regulatory dynamics of mouse nephron progenitors [ChIP-seq]

Project description:Single-cell chromatin and gene-regulatory dynamics of mouse nephron progenitors [ChIP-seq]

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Chromatin and gene-regulatory dynamics of mouse nephron progenitors at single-cell resolution

Project description:Chromatin and gene-regulatory dynamics of mouse nephron progenitors at single-cell resolution

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2024-07-31 | GSE264518 | GEO

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