Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SINGLE CELL ANALYSIS OF POLYCYSTIC KIDNEY DISEASE USING HUMAN PLURIPOTENT STEM CELL- DERIVED KIDNEY ORGANOIDS

ABSTRACT: To reveal the key pathways involved in kidney cystogenesis. We performed single nuclei gene expression and ATAC profiling using kidney organoids from ARPKD patients-iPSCs derived organoids.

ORGANISM(S): Homo sapiens

PROVIDER: GSE244608 | GEO | 2023/10/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

MODELLING GENETIC POLYCYSTIC KIDNEY DISEASE USING HUMAN PLURIPOTENT STEM CELL- DERIVED KIDNEY ORGANOIDS

Project description:To investigate the transcriptional features during cystogenesis, we performed bulk-RNA sequencing on ARPKD organoids. We then performed gene expression profiling and Gene Set Enrichment Analysis using data obtained from bulk RNA-seq.

2023-05-08 | GSE231591 | GEO

Generating Patterned Kidney Organoids for Studying Development and Diseases [scRNA-Seq]

Project description:Human pluripotent stem cells (hPSCs)-derived kidney organoids recapitulate complex developmental processes and tissue architectures, but the intrinsic limitations, such as variability and a lack of vasculature, have greatly hampered their application. Here we establish a highly efficient and versatile protocol for generating vascularized three-dimensional (3D) kidney organoids. We employ dynamic modulation of WNT signaling to control the relative proportion of proximal versus distal nephron segments, thereby producing a correlative level of VEGFA to define the resident vascular network. By single cell RNA-sequencing, we identify a subset of nephron progenitor cells as a potential source of the vasculature. Upon implantation into host mice, these kidney organoids undergo further structural and functional maturation, as demonstrated by the size-selective handling of dextran. Based on this differentiation platform, we establish an in vitro model of autosomal recessive polycystic kidney disease (ARPKD) by differentiating induced PSCs (iPSCs) from an ARPKD patient into 3D kidney organoids that develop tubule cysts in response to cAMP upregulation. The cystogenesis phenotype can be effectively prevented by gene correction or drug treatment. Our studies provide a versatile platform for studying human kidney development and diseases, and opens new avenues for modeling disease pathogenesis and performing patient-specific drug screening.

2019-06-01 | GSE132023 | GEO

Generating Patterned Kidney Organoids for Studying Development and Diseases [bulk RNA-Seq]

2019-05-29 | GSE131841 | GEO

Human pluripotent stem cell-derived kidney organoids reveal tubular epithelial pathobiology of heterozygous HNF1B-associated dysplastic kidney malformations CL

Project description:Hepatocyte nuclear factor 1B (HNF1B) encodes a transcription factor expressed in developing human kidney epithelia. Heterozygous HNF1B mutations are the commonest monogenic cause of dysplastic kidney malformations (DKMs). To understand their pathobiology, we generated heterozygous HNF1B mutant kidney organoids from CRISPR-Cas9 gene-edited human ESCs and iPSCs reprogrammed from a family with HNF1B-asscociated DKMs. Mutant organoids contained enlarged malformed tubules and displayed deregulated cell turnover. This submission is RNAseq of organoids from MAN13 embryonic stem cells.

2024-04-29 | E-MTAB-12824 | biostudies-arrayexpress

Human pluripotent stem cell-derived kidney organoids reveal tubular epithelial pathobiology of heterozygous HNF1B-associated dysplastic kidney malformations K

2024-04-29 | E-MTAB-12822 | biostudies-arrayexpress

Expression data from polycystic kidney disease susceptible and resistant rat strains

Project description:To facilitate the search for genetic modifiers that modulate ARPKD disease progression and severity, we sought to generate a congenic rat model that carries the PCK Pkhd1 mutation but is resistant to the development of ARPKD. We transferred the Pkhd1 mutation from the PCK rat onto the genetic background of the FHH (Fawn-Hooded Hypertensive) rat. This newly developed strain, called FHH.Pkhd1, showed significant amelioration of renal disease, and delayed onset of biliary abnormalities. To initiate the exploration for genes and pathways that modulate susceptibility to renal cystogenesis, we investigated transcriptional changes in kidneys from PCK, SD, FHH and FHH.Pkhd1 rats by microarray analysis. Both kidneys were harvested from 6 animals for each strain; SD, FHH, PCK, FHH.Pkhd1 (FHH.PCK-(D9Rat35-D9Rat70)/Mcwi, RGD ID 5147594) at 30 days of age. The kidneys were bisected and stored in RNAlater at 4C for 24hrs. RNA was extracted using the Trizol (Invitrogen) method according to manufacturer’s instructions. RNA from each strain was pooled together, reverse transcribed, and hybridized to three Affymetrix Rat 230 arrays (Affymetrix).

2012-01-01 | E-GEOD-33056 | biostudies-arrayexpress

Expression data from polycystic kidney disease susceptible and resistant rat strains

2012-01-01 | GSE33056 | GEO

Next Generation Sequencing Technologies to Investigate Autosomal Recessive Polycystic Kidney Disease (ARPKD).

Project description:Autosomal Recessive Polycystic Kidney Disease (ARPKD) is a rare paediatric disease primarily caused by mutations in the gene PKHD1. ARPKD presents with considerably clinical variability which is linked to the type of PKHD1 mutation but not position. Animal models of Polycystic Kidney Disease (PKD) suggest there is a complex genetic landscape with genetic modifiers as a potential cause of disease variability. Transcriptomic analysis identified a considerable number of genes linked to cellular metabolism and development. Amongst these genes were those linked to WNT signalling. Two individuals in this cohort had the same mutations in PKHD1 but different rates of kidney disease progression. Amongst the transcriptomic differences of these two individuals were differences in the expression changes of WNT genes.

2024-09-06 | GSE242476 | GEO

LC MS/MS of kidney organoids during differentiation from day 21 to 29

Project description:Kidney organoids are a valuable and innovative model to understand genetic diseases, kidney development and transcriptomic dynamics. However, their proteome has not been analyzed so far. Here, we analyzed the organoid proteome trajectory during differentiation. Genes involved in podocytopathies and cystic kidney diseases were abundantly expressed on protein level, distinguishing organoids from almost every available cell culture model. On their pathway to terminal differentiation, organoids developed increased deposition of extracellular matrix. Single cell transcriptomic analysis suggests that most changes locate to podocytes and early podocyte progenitors. This matrix deposition is different from commonly used animal models of glomerular disease. We grew organoids from two independent batches according to the Freedman protocol, and performed proteomic profiling (Freedman, Brooks et al. 2015, Czerniecki, Cruz et al. 2018). The IPSCs were differentiated for a three-week period until first spheroids from. From day 21 of the culture they were used in our experiments up until day 29, where off-target differentiation of organoids becomes an issue.

2023-05-12 | PXD029716 | Pride