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TFAP2A orchestrates gene regulatory networks and tubular architecture in kidney outer medullary collecting ducts [bulk RNA-seq]

ABSTRACT: TFAP2A orchestrates gene regulatory networks and tubular architecture in kidney outer medullary collecting ducts [bulk RNA-seq]

PROVIDER: PRJNA1191370 | ENA |

REPOSITORIES: ENA

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TFAP2A orchestrates gene regulatory networks and tubular architecture in kidney outer medullary collecting ducts.

Project description:Mutations of the transcription factor TFAP2A are associated with congenital anomalies of the kidney and urinary tract in humans. In mice, deficiency of its ortholog Tfap2a in collecting duct cells causes widened epithelial tubules in the outer medulla of the adult kidney, but the molecular mechanisms of this phenotype are unknown. In this study, we identified gene regulatory networks controlled by Tfap2a in mouse kidney collecting ducts by combining gene knockout and transcriptomics. Integrated analyses of single-nucleus and bulk RNA-sequencing data from kidneys of adult Tfap2a knockout and control mice indicated deregulated expression of genes associated with cell adhesion and Wnt signaling pathways. Validation studies revealed that Tfap2a controls Wnt9b and Alcam, known regulators of kidney tubule morphogenesis. Our data provide novel insights into kidney epithelial gene regulatory networks controlled by Tfap2a and its potential functional role in congenital renal disease.

2025-08-08 | GSE290794 | GEO

TFAP2A orchestrates gene regulatory networks and tubular architecture in kidney outer medullary collecting ducts [bulk RNA-seq]

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TFAP2A orchestrates gene regulatory networks and tubular architecture in kidney outer medullary collecting ducts.

Project description:TFAP2A orchestrates gene regulatory networks and tubular architecture in kidney outer medullary collecting ducts.

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Gene expression profile of zebrafish renal collecting ducts

Project description:The kidney is the main hematopoietic organ in teleost fish. Various stages of hematopoietic cells were observed in the interstitial tissue of the kidney. We recently demonstrated that zebrafish hematopoietic stem cells (HSCs) expressing jam1a were specifically localized along the renal collecting ducts in the adult kidney. Interestingly, most of HSCs invaded into the intracellular spaces of the epithelium in collecting ducts, suggesting that collecting ducts provide a specific microenvironment for HSCs. In order to identify niche factors in collecting ducts, we performed microarray analysis in collecting ducts isolated from the Tg(jam1a:EGFP) zebrafish kidney. Collecting ducts were isolated from Tg(jam1a:EGFP) zebrafish under a fluorescent microscope. To examine the effect of X-ray irradiation on the niche, collecting ducts were isolated from the fish irradiated with 25Gy. The whole kidney tissues were also used for a comparison analysis. Two independent replicates consisting of five zebrafish were prepared for each sample.

2012-08-24 | E-GEOD-32363 | biostudies-arrayexpress

Gene expression profile of zebrafish renal collecting ducts

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Transcriptomic Analysis of Outer Medullary Collecting Duct (OMCD) from mice under control or high-Salt diet.

Project description:We applied RNAseq analysis on microdissected outer medullary collecting duct renal segments from mice fed a normal (0.3% Na+) or high Na+ (3%) diet for 3 days. Among 11688 genes sequenced, 293 have an expression significantly modified (p<0.05), 78 with a -1<log2FC>1. In addition to expected results like the decreased expression of genes participating at the Na+ reabsorption (Scnn1a, SGK1), we observed the stimulation of ATP12a gene that participate at a recently described Na+ secretion pathway.

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Targeted proteomics analysis of cortical collecting ducts with Pendrin knockout

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Trancriptome profiling of rat inner medullary collecting duct

Project description:Identification of gene expressed in the enriched inner medullary collecting duct cells in rat. Keywords: gene expression comparision between cell type

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Transcription profiling of rat inner medullary collecting duct

Project description:Identification of gene expressed in the enriched inner medullary collecting duct cells in rat. Experiment Overall Design: Rat inner medullary collecting duct (IMCD) cells were isolated from 7 male Sprage-Dawley rats by collagenase and hyaluronidase digestion and follow by low speed centrifugation. The non-IMCD cells were collected by centrifugation of supernatant of enriched IMCD samples. Experiment Overall Design: Total RNA about 3 ug were used per microarray (Rat 230 2.0 Genechip array). Experiment Overall Design: The experiments were repeat 3 times (3 pairs of IMCD VS non-IMCD)

2008-06-15 | E-GEOD-7891 | biostudies-arrayexpress

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