Similar Datasets
Project description:The goal of our study is to determine if interstitial Notch signaling is required for the formation/development of nephron segments.
2025-02-19 | GSE202882 | GEO
Project description:In this study, in order to better understand shared core Hox functions, we examined kidney development in mice with frameshift mutations of multiple Abd-B type Hox genes. The resulting phenotypes included dramatically reduced branching morphogenesis of the uretreric bud, premature depletion of nephron progenitors and abnormal development of the stromal compartment. Most unexpected, however, we also observed a cellular level lineage infidelity in nephron segments.
2018-01-20 | GSE109404 | GEO
Project description:To gain molecular insight into kidney function, we performed a high-resolution quantitative analysis of gene expression in glomeruli and nine different nephron seg-ments dissected from mouse kidney using the long-SAGE method. We also developed dedicated bioinformatics tools and databases to annotate mRNA tags as transcripts. Over 800,000 mRNA SAGE tags were sequenced corresponding to >20,000 different mRNA tags present at least twice in at least one library. Hierarchical clustering analysis of tags demonstrated similarities between the three anatomical sub-segments of the proximal tubule, between the cortical and medullary segments of the thick ascending limb of Henle’s loop, and between the three segments constituting the aldosterone sensitive distal nephron segments, whereas the glomerulus and distal convoluted tubule clusterized independently. We also identified highly specific mRNA markers of each subgroup of nephron segments and of most nephron segments. Tag annotation also identified numbers of putative antisense mRNAs. This database constitutes a reference resource in which the quantitative expression of a given gene can be compared with that of other genes in the same nephron segment, or between different segments of the nephron. To illustrate possible applications of this database, we performed a deeper analysis of the glomerulus transcriptome which unexpectedly revealed expression of several ion and water carriers; within the glomerulus, they were found to be preferentially expressed in the parietal sheet. It also revealed the major role of the zinc finger transcription factor Wt1 in the specificity of gene expression in the glomerulus. Finally, functional annotation of glomerulus-specific transcripts showed the high proliferation activity of glomerular cells. Immunolabelling with anti-PCNA antibodies confirmed a high percentage of proliferating glomerular parietal cells. Approximately 1000 tubules from each different nephron segments were microdissected from 6-8 male CD1 mice. Over 800,000 mRNA SAGE tags were sequenced corresponding to >20,000 different mRNA tags present at least twice in at least one library.
2010-11-11 | E-GEOD-25223 | biostudies-arrayexpress
Project description:To gain molecular insight into kidney function, we performed a high-resolution quantitative analysis of gene expression in glomeruli and nine different nephron seg-ments dissected from mouse kidney using the long-SAGE method. We also developed dedicated bioinformatics tools and databases to annotate mRNA tags as transcripts. Over 800,000 mRNA SAGE tags were sequenced corresponding to >20,000 different mRNA tags present at least twice in at least one library. Hierarchical clustering analysis of tags demonstrated similarities between the three anatomical sub-segments of the proximal tubule, between the cortical and medullary segments of the thick ascending limb of Henle’s loop, and between the three segments constituting the aldosterone sensitive distal nephron segments, whereas the glomerulus and distal convoluted tubule clusterized independently. We also identified highly specific mRNA markers of each subgroup of nephron segments and of most nephron segments. Tag annotation also identified numbers of putative antisense mRNAs. This database constitutes a reference resource in which the quantitative expression of a given gene can be compared with that of other genes in the same nephron segment, or between different segments of the nephron. To illustrate possible applications of this database, we performed a deeper analysis of the glomerulus transcriptome which unexpectedly revealed expression of several ion and water carriers; within the glomerulus, they were found to be preferentially expressed in the parietal sheet. It also revealed the major role of the zinc finger transcription factor Wt1 in the specificity of gene expression in the glomerulus. Finally, functional annotation of glomerulus-specific transcripts showed the high proliferation activity of glomerular cells. Immunolabelling with anti-PCNA antibodies confirmed a high percentage of proliferating glomerular parietal cells.
2010-11-11 | GSE25223 | GEO
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.
2020-11-19 | GSE149134 | GEO
Project description:The proximal tubule (PT) is a highly energetic segment of the nephron, responsible for the majority of solute and water reabsorption in the kidney. Each of its sub-segments have specialized functions; however, little is known about the genes and proteins that determine the oxidative phosphorylation capacity of the PT sub-segments. This information is a critical deficit in understanding kidney function and to develop a fuller comprehensive landscape of renal cell adaptations to injury, toxins, physiologic stressors, and development. In this study, three immortalized murine renal cell lines (PT S1,S2 and S3 segments) were analyzed for protein content and compared to a murine fibroblast cell line. All three proximal tubule cell lines generate ATP predominantly by oxidative phosphorylation while the fibroblast cell line is glycolytic. The proteomic data demonstrates that the most striking difference in proteomic signatures between the cell lines are differences in nuclear proteins followed by differences in mitochondria proteome. The mitochondria physiologic profile is also determined in the cell lines to provide physiologic context to the proteomic dataset. This data set will allow researchers to study differences in nephron-specific cell lines, differences between epithelial and fibroblast cells, and differences between actively respiring cells and glycolytic cells.
2022-07-07 | MSV000089838 | MassIVE
Project description:Our laboratory's interest is in understanding the molecular principles that underlie the regional organization of the mammalian metanephric kidney. Our goal is to generate a detailed spatial map of the cellular expression of selected regulatory genes during mammalian kidney development. The goal of this study is to identify genes expressed during the morphogenesis of the nephron. By profiling two specific developmental nephron structures, we expect to identify genes expressed in both, and unique to each, which suggests they may play a role in the underlying mechanism responsible for the morphogenesis. Experiment Overall Design: Two early nephron structures, the renal vesicle and the s-shaped body, and the collecting duct system, were microdissected from E14.5 kidneys based on morphological criteria. Antibody and lectin staining together with RT-PCR were used for identity verification and for exclusion of contamination by other tissues. Samples are minimally pooled for amplification. A biological replicate is a single minimally pooled sample. RNA isolated from the collected structures was put through two rounds of T7-driven amplification to obtain the microgram quantities of cRNA needed for hybridization to Affymetrix microarrays. Detection of genes previously shown to be expressed in these early structures, such as Wt1, Wnt4 and Pax8, validates the data from the screen. The collecting duct sample serves as a reference sample for comparing the renal vesicle and s-shaped body comparison in this study.
2008-06-14 | E-GEOD-6287 | biostudies-arrayexpress
Project description:Early human kidney development is poorly documented due to tissue inaccessibility and a lack of genetic tractability. Here we combine reprogramming, CRISPR/Cas9 gene-editing and organoid technologies to study the nephron lineage in a human context. We confirm the presence of a SIX2+ population in early kidney organoids with a transcriptional profile akin to human fetal nephron progenitors. Using lineage-tracing analyses, we show that SIX2-expressing cells contribute to nephron formation but not to the putative collecting duct epithelium. Labeling of SIX2+ cells at various time-points during organoid differentiation revealed a markedly reduced capacity for these cells to contribute to nephron formation over time. This suggests human kidney organoids lack a true nephron progenitor niche, as the developing kidney does in vivo, capable of both self-renewal and ongoing nephrogeneis. Nonetheless, human iPSC-derived kidney tissue maintains previously identified lineage relationships, which supports the utility of in vitro organoid models for interrogating the molecular and cellular basis of early human development.
2019-03-12 | GSE119561 | GEO
Project description:Improved specification of metanephric nephron progenitors in conditions that prolong differentiation while simultaneously preventing spontaneous nephron induction resulted in proximal tubule (PT)-enhanced kidney organoids. PT-enhanced organoids exhibited improved PT maturation, with elongated and aligned nephron segments as well as distinct loops of Henle. The striking proximo-distal orientation of nephrons was shown to result from localised WNT antagonism originating from the centre of the organoid.
2022-08-25 | GSE184928 | GEO
Project description:Our laboratory's interest is in understanding the molecular principles that underlie the regional organization of the mammalian metanephric kidney. Our goal is to generate a detailed spatial map of the cellular expression of selected regulatory genes during mammalian kidney development. The goal of this study is to identify genes expressed during the morphogenesis of the nephron. By profiling two specific developmental nephron structures, we expect to identify genes expressed in both, and unique to each, which suggests they may play a role in the underlying mechanism responsible for the morphogenesis. Keywords: kidney component comparison
2006-11-18 | GSE6287 | GEO