Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic analysis of microdissected renal tubules

ABSTRACT: Kidney is a vital organ which help maintain body homeostasis. Three related processes including glomerular filtration, tubular reabsorption and secretion are precisely regulated in the kidney in response to changes in the amount of both water and various solutes. To understand how the kidney can achieve this challenging goal, it is important to know the protein composition in the kidney. However, unlike other solid organs, kidney has a very intricate architecture, including at least 14 distinct tubule segments. This reason limits the interpretibility of experiments perfomred using whole kidney homegenate samples. To mitigate this problem, we combined kidney tubule microdissection technique with protein mass spectrometry to study the proteome of 14 individual rat kidney tubule segment.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Kidney

DISEASE(S): Disease Free

SUBMITTER: Kavee Limbutara

LAB HEAD: Mark A. Knepper

PROVIDER: PXD016958 | Pride | 2020-04-20

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Quantitative Proteomics of All 14 Renal Tubule Segments in Rat.

Limbutara Kavee K Chou Chung-Lin CL Knepper Mark A MA

Journal of the American Society of Nephrology : JASN 20200501 6

<h4>Background</h4>Previous research has used RNA sequencing in microdissected kidney tubules or single cells isolated from the kidney to profile gene expression in each type of kidney tubule epithelial cell. However, because proteins, not mRNA molecules, mediate most cellular functions, it is desirable to know the identity and amounts of each protein species to understand function. Recent improvements in the sensitivity of mass spectrometers offered us the ability to quantify the proteins expre ...[more]

PMID: 32358040

Similar Datasets

Transcription profiling of Drosophila pooled Malpighian tubules vs. whole fly

Project description:This is an affymetrix array experiment comparing the transcriptome of the Malpighian tubule (or renal tubule) of 7-day adult Oregon R strain Drosophila melanogaster with matched whole fly samples. It is described in:,Wang, J., Kean, L., Yang, J., Allan, A. K., Davies, S. A., Herzyk, P. and Dow, J. A. T. (2004). Function-informed transcriptome analysis of Drosophila renal tubule. Genome Biol. In press.,There are five tubule samples (each derived from approx 1000 tubules (!)), and 5 matched whole-fly samples. i.e. tubule 2 is dissected from the same vial as WholeFly2.,As the tubule is probably the premier tissue for true physiology in Drosophila, the dataset can usefully be interrogated in conjunction with the detailed physiological understanding of the tissue: see,http://fly.to/tubules

2007-07-06 | E-GEOD-1690 | biostudies-arrayexpress

PPARs and c-Myc regulate metabolism of renal tubules

Project description:Different segments of renal tubules have distinct metabolic features and functions, and defective metabolism in renal tubules is involved in the pathobiology of kidney diseases. However, the mechanisms underlying the metabolic regulation in renal tubules remain to be defined. We demonstrated that the renal proximal tubule (PT) has high expression of fatty acid and lipid metabolism enzymes, which is transcriptionally upregulated by abundantly expressed peroxisome proliferator-activated receptor (PPAR)/γ to support active lipid metabolism. In contrast, the renal distal tubule (DT) has elevated glycolytic enzyme expression corresponding with high rates of glycolysis, and this increased expression is mediated by abundantly expressed c-Myc. In addition, Nrf2 upregulated glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, and NADP-dependent malic enzyme 1 expression for NADPH production and antioxidation in the DT. Highly expressed PPARγ transcriptionally enhanced expression of the protease iRhom2 in the PT, which suppressed epidermal growth factor (EGF) expression and secretion, inhibiting EGF receptor activation-dependent glycolytic gene expression and maintaining the low level of glycolysis. PPARγ inhibition reduced iRhom2 expression and increased EGF and GLUT1 expression in the PT in mice, resulting in hypertrophy of renal tubules and inhibited kidney functions, which can be rescued by inhibition of glycolysis via treatment with 2-deoxy-D-glucose. These findings delineate instrumental molecular mechanisms underlying the active lipid metabolism and suppressed glycolysis in the PT and active glycolysis in the DT and reveal critical roles for PPARs and c-Myc in maintaining metabolic homeostasis in the kidney

2018-11-15 | PXD007828 | Pride

Methylation Profiling of Human Kidney Tubules

Project description:We sought to decrease the cell type heterogeneity of kidney tissues to increase the resolution of methylation profiles. To that end, microdissected human kidney tissue from patients are used and hybridized on Illumina HumanMethylation450 BeadChip arrays. We extract genomic DNA from microdissected human kidney tubule samples. And used these genomic DNA for the Illumina 450K beads array.

2013-09-14 | E-GEOD-50874 | biostudies-arrayexpress

RNA-seq profiling of microdissected rat renal tubule segments

Project description:We sequenced mRNAs from glomeruli and 14 different rat renal tubule segments collected by hand microdissection. Collagenase-digested rat renal tubule segments were collected by hand microdissection. Poly(A)-mRNAs were captured from cell lysate and sequenced using paired-end protocol.

2015-03-31 | E-GEOD-56743 | biostudies-arrayexpress

Transcription profiling of cortical collecting duct/connecting nephron tissue from mice treated with aldosterone, canrenoate vs. controls to identify gene products regulated by aldosterone in target cells

Project description:The mineralocorticoid hormone aldosterone controls sodium reabsorption and blood pressure largely by regulating the cell-surface expression and function of the epithelial sodium channel ENaC in target kidney tubules. Part of the stimulatory effect of aldosterone on ENaC is mediated by the induction of SGK1, a kinase that interferes with the ubiquitylation of ENaC by ubiquitin-protein ligase Nedd4-2. We performed a microarray study in order to investigate which other gene products are rapidly regulated by aldosterone in target cells that participate to the control of Na+ reabsorption and K+ secretion.

2007-03-07 | E-TABM-229 | biostudies-arrayexpress

Transcriptome Changes of Microdissected Kidney Tubules triggered by Unilateral Nephrectomy [RNA-seq]

Project description:Purpose: Experiments were done in mice undergoing unilateral nephrectomy (UNx) and sham nephrectomy. At specific time points (24 hours and 72 hours) after surgery, the earliest first portion of the kidney proximal tubule (PT-S1) and the cortical collecting duct (CCD) were manually micro-dissected and utilized for transcriptomic analysis by single-tubule small sample RNA-Seq. Methods: We carried out RNA-sequencing in microdissected ealiest portion of proximal tubules (PT-S1) or cortical collecting duct (CCD) from mice with or without (sham) unilateral nephrectomy (UNx). Each group (Sham or UNx) has 3-5 biological replicates. Results and conclusion: RNA-Seq in microdissected PT-S1 at 24 hours showed that peroxisome proliferator-activated receptor alpha (PPARα) target genes were strongly upregulated. RNA-Seq in microdissected PT-S1 at 72 hours showed that cell cycle related genes were strongly upregulated. RNA-Seq in microdissected CCD at both 24 hours and 72 hours showed that cell cycle related genes were strongly upregulated.

2022-08-14 | GSE211021 | 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

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

SY-85-Microarray-KidneyGE-Profiling

Project description:We performed genome wide transcriptome analyses of a large cohort human kidney tubule samples.

2014-04-15 | E-MTAB-2502 | biostudies-arrayexpress

Spectral library for targeted analysis of mouse kidney cortical collecting duct

Project description:We generated a spectral library of kidney cortical collecting ducts (CCD) using data-dependent proteomics acquisition.

2020-12-21 | PXD018795 | Pride