Molecular detection of maturation stages in the developing kidney
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA643510 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12125424.fastq.gz | Fastqsanger.gz | |||
| SRR12125425.fastq.gz | Fastqsanger.gz | |||
| SRR12125426.fastq.gz | Fastqsanger.gz | |||
| SRR13080698_1.fastq.gz | Fastqsanger.gz | |||
| SRR13080698_2.fastq.gz | Fastqsanger.gz |
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Project description:To identify maturation-dependent genes, we here performed single cell RNA sequencing (scRNA-seq) analysis using developing kidneys at different stages in the mouse, followed by highly sensitive in situ hybridization. We identified multiple genes expressed abundantly in newborn kidneys, but minimally at embryonic day 15.5. We then applied these maturation markers to the transplanted embryonic kidneys and found that the maturation process did not occur equally throughout nephron segments upon transplantation: glomeruli and proximal renal tubules became more mature than the other nephron segments. Thus, our scRNA-seq data at multiple stages of kidney development and identified maturation-dependent genes will serve as useful bases for assessing maturation of the developing kidney, and eventually of kidney organoids.
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Project description:Kidney organoids are connected to the host circulation and mature after transplantation. However, they are still immature compared to the adult kidneys, and their precise maturation stages remain unclear. By transplanting the mouse embryonic kidney as a model system for organoid transplantation, we report here the maturation defects of the graft, especially in the medulla. Single cell profiling of the developing kidneys in vivo identified gene sets associated with the maturation of the collecting duct epithelium and medullary stroma. These data revealed an upregulation of genes associated with channel/transporter functions and immune defense, as well as a downregulation of neuronal genes. Using these marker genes, we found that the maturation of the collecting duct and medullary stroma in the grafts barely corresponds to the perinatal stage, which was confirmed histologically by using representative genes. Thus, the gene sets obtained serve as maturation coordinates for the renal medulla and will be helpful in analyzing its maturation defects after transplantation. They will also provide a useful basis for further maturation of transplanted kidney organoids.
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Project description:To characterize the molecular features of human kidney development, and to capture timing of emergence of important kidney compartments, we generated mRNA-Seq data from human kidneys at various developing stages. In order to capture tissue representing the entire kidney, we sampled kidneys with a wedge spanning from the cortex to medulla region.
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Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. Experiment Overall Design: At specific developmental time points we isolate discrete elements of the kidney by using fluorescent activated cell sorting (FACS) and then define their gene expression profiles with microarrays.
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