Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function

ABSTRACT: We used bulk and single-cell ATAC-seq to measure chromatin accessibilty in human kidneys. This allowed us to define candidate cis-regulatory elements of each human kidney cell type and identify the role of podocyte and tubule regulatory elements in human kidney function.

ORGANISM(S): Homo sapiens

PROVIDER: GSE262931 | GEO | 2024/07/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function

Project description:Kidney failure, the decrease of kidney function below a threshold necessary to support life, is a major cause of morbidity and mortality in humans. Kidney function is highly heritable; yet, the cellular and molecular mechanisms which contribute to differences in human kidney function remain obscure. We performed a genome wide association study (GWAS), identifying 430 loci affecting kidney function in middle-aged adults. To investigate which cell types are affected by these loci, we integrated the GWAS with human kidney candidate cis-regulatory elements (cCREs), identified using scATAC-seq. 56% of kidney function heritability localized to kidney tubule epithelial cCREs and an additional 7% to kidney podocyte cCREs. Thus, most of the heritable differences in adult kidney function is due to altered gene expression in these two cell types. Using enhancer assays, allele-specific scATAC-seq and machine learning, we found that many kidney function variants alter cCRE chromatin accessibility and function. Using CRISPRi, we determined which genes some of these cCREs regulate, implicating NDRG1, CCNB1 and STC1 in human kidney function. This work provides an experimental approach to identify the variants, regulatory elements and genes involved in human traits and disease.

2024-07-15 | GSE266319 | GEO

Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function

Project description:Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function

| PRJNA1106741 | ENA

Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function

Project description:Variants in tubule epithelial regulatory elements mediate most heritable differences in human kidney function

| PRJNA1094933 | ENA

Histone tail modification profiles of human renal tubule epithelial cells

Project description:To annotate the regulatory elements in the renal tubule epithelial cells, we profiled 6 histone ChIP-seq in the human kidney epithelical cells (HKC8). We pulled down the DNA with specific antibodies of interests against histone tail modifications in the human rebal tubule epithelial cells. The result can be interpretated with ChromHMM for different states.

2013-08-09 | E-GEOD-49637 | biostudies-arrayexpress

Histone tail modification profiles of human renal tubule epithelial cells

Project description:To annotate the regulatory elements in the renal tubule epithelial cells, we profiled 6 histone ChIP-seq in the human kidney epithelical cells (HKC8).

2013-08-09 | GSE49637 | GEO

Profiling of Transcripts in Rat Proximal Tubule

Project description:Freshly isolated rat kidney proximal tubules were subjected for transcript profiling. Three microarray experiments were done to obtain the kidney proxmial tubule transcriptome.

2009-01-26 | E-GEOD-13668 | biostudies-arrayexpress

Predicting drivers of proximal tubule cell state through regularized regression analysis of single cell multiomic sequencing

Project description:In this study, we generated a single nucleus multiomic (snRNA-seq and snATAC-seq) dataset of adult human kidney. We developed a bioinformatic tool to analyze this dataset by identifying key cis-regulatory elements and transcription factors associated with specific cell types and states. We applied this tool to identify transcription factors implicated in proximal tubule cell injury and failed repair states. We demonstrate this tool can be applied to single cell multiomic datasets to derive insight into cell type- and state-specific gene regulatory networks.

2023-01-02 | GSE220230 | GEO

Predicting drivers of proximal tubule cell state through regularized regression analysis of single cell multiomic sequencing

2023-01-02 | GSE220222 | GEO

Effect of GW4064 on primary cultured mouse kidney proximal tubule cells

Project description:Global gene expression in the primary cultured mouse kidney proximal tubule cells treated either DMSO or 1uM GW4064 (a FXR agonist) was compared. Results provide insight into mechanisms underlying effects of FXR activation on gene expression in mouse kidney proximal tubule cells. Male C57/BJ mice aged 6 weeks were sacrificed under anesthesia and kidney proximal tubule cells were cultured until confluent. Cells were treated with either GW4064 (1uM) or equal amount of DMSO and incubated for 24 hours. 4 total RNA samples per group were analyzed and gene expression was compared between the groups.

2015-06-26 | E-GEOD-70296 | biostudies-arrayexpress

Expression data from human kidney tubule epithelial cells

Project description:Expression data from human kidney tubule epithelial cells

| PRJNA494100 | ENA