Transcriptomic Analysis of Outer Medullary Collecting Duct (OMCD) from mice under control or high-Salt diet.
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ABSTRACT:
PROVIDER: PRJNA1023847 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26277066_1.fastq.gz | Fastqsanger.gz | |||
| SRR26277066_2.fastq.gz | Fastqsanger.gz | |||
| SRR26277067_1.fastq.gz | Fastqsanger.gz | |||
| SRR26277067_2.fastq.gz | Fastqsanger.gz | |||
| SRR26277068_1.fastq.gz | Fastqsanger.gz |
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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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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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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)
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Project description:The affect of aldosterone on the miRNA landscape in mIMCD-3 cells was determined In the study presented here, the affect of aldosterone was examined on the miRNA content in a murine inner medullary collecting duct cell line
2014-05-31 | E-GEOD-47901 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to identify doxycycle-responsive genes in mouse kidney inner medullary collecting duct cell line mIMCD3. To explore compreshensive profile of doxycycline-mediated gene expression, transcriptomes of doxycycline-responsive genes at two different time points (3 days and 6 days) were profiled and analyzed. Methods: Total RNAs were isolated from mIMCD3 cells treated with doxycycline or vehicle at different time points (3 days and 6 days). Four replicates for vehicle- or doxycycline-treated group were generated at each tested time point. cDNA libraries were prepared using a Nextera DNA library preparation protocol. The sequence reads from Illumina HiSeq3000 platform were qualified and quantified at the transcript level using Salmon (0.14.1). Differential expression analysis were performed using edgeR. Results: mRNA profiles of mouse kidney inner medullary collecting duct mIMCD3 cells treated with doxycycline or vehicle (DMSO) for 3 days and 6 days were generated using an optimized RNA-Seq workflow. Transcript level quantification using a pseudo-alignment quantification method (Salmon) was performed to calculate transcript abundance in each sample. Then differential expression analysis identified the differentially expressed genes at each time point comparison (DOX vs vehicle). Conclusions: This study revealed comprehensive transcriptomic changes of doxycycline-responsive gene expression in mouse kidney inner medullary collecting duct cells.
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Project description:Murine inner medullary collecting duct cells were treated for 1 hour with vehicle (control) or aldosterone. Total RNA was isolated and used as template to generate the eventual cRNA target. The experiment was repeated a total of three times. Six cRNA samples, three control and three treated, were generated and used in a total of six hybridizations. The mineralocorticoid aldosterone is a major regulator of Na+ and acid-base balance and control of blood pressure. Although the long-term effects of aldosterone have been extensively studied, the early aldosterone-responsive genes remain largely unknown. Using DNA array technology, we have characterized changes in gene expression after 1 h of exposure to aldosterone in a mouse inner medullary collecting duct cell line, mIMCD-3. Results from three independent microarray experiments revealed that the expression of many transcripts was affected by aldosterone treatment. Northern blot analysis confirmed the upregulation of four distinct transcripts identified by the microarray analysis, namely, the serum and glucose-regulated kinase sgk, connective tissue growth factor, period homolog, and preproendothelin. Immunoblot analysis for preproendothelin demonstrated increased protein expression. Following the levels of the four transcripts over time showed that each had a unique pattern of expression, suggesting that the cellular response to aldosterone is complex. The results presented here represent a novel list of early aldosterone-responsive transcripts and provide new avenues for elucidating the mechanism of acute aldosterone action in the kidney. Keywords: other
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Project description:Regulation of renal water excretion is dependent on control of the molecular water channel aquaporin‐2 by the peptide hormone vasopressin in renal collecting duct cells. The control is in part due to the regulation of transcription of the Aqp2 gene and other genes by vasopressin. A systems biology‐based approach to understanding transcriptional control in renal collecting duct cells depends on knowledge of what transcription factors and other regulatory proteins are present in the cells' nucleus. The goal of this paper is to report comprehensive proteomic profiling of nuclear proteins in native inner medullary collecting duct (IMCD) cells of the rat. Multi‐dimensional separation procedures and state‐of‐the art protein mass spectrometry allowed the high stringency identification of a total of 5105 proteins in nuclear pellet (NP) and nuclear extract (NE) fractions of biochemically isolated rat IMCD cells (URL: https://helixweb.nih.gov/ESBL/Database/IMCD_Nucleus/)*. The analysis identified 369 transcription factor proteins out of the 1371 transcription factors coded by the rat genome. The analysis added 1898 proteins to the recognized proteome of rat IMCD cells, now amounting to 7003 unique proteins. Analysis of samples treated with the vasopressin analog dDAVP (1 nM for 30min) or its vehicle revealed 99 proteins in the NP fraction and 88 proteins in the NE fraction with significant changes in spectral counts (Fisher Exact Test, P<0.005). Among those altered by vasopressin were 7 distinct histone proteins all of which showed decreased abundance in the NP fraction, consistent with a possible effect of vasopressin to induce chromatin remodeling.
2018-10-24 | PXD002680 | Pride
Project description:Libraries obtained from microdissected kidney outer medullary collecting duct from C57Bl6/J mice control or after 3 days potassium-depleted diet. Keywords: other
2004-05-30 | E-GEOD-1445 | biostudies-arrayexpress
Project description:Libraries obtained from microdissected kidney outer medullary collecting duct from C57Bl6/J mice control or after 3 days potassium-depleted diet. Keywords: other
2004-05-30 | GSE1445 | GEO
Project description:Kidneys are essential for acid-base homeostasis, especially when organisms cope with changes in acid or base dietary intake. Because collecting ducts constitute the final site for regulating urine acid-base balance, we undertook to identify the gene network involved in acid-base transport and regulation in the mouse outer medullary collecting duct (OMCD). For this purpose, we combined kidney functional studies and quantitative analysis of gene expression in OMCDs, by transcriptome and candidate gene approaches, during metabolic acidosis. Furthermore, to better delineate the set of genes concerned with acid-base disturbance, the OMCD transcriptome of acidotic mice was both compared to that of normal mice and mice undergoing an adaptative response through potassium depletion. Metabolic acidosis, achieved through a NH4Cl-supplemented diet for 3 days, not only induced acid secretion, but also stimulated the aldosterone and vasopressin systems and triggered cell proliferation. Accordingly, metabolic acidosis increased the expression of genes involved in acid-base transport, sodium transport, water transport and cell proliferation. In particular, more than 25 transcripts encoding proteins involved in urine acidification (subunits of H-ATPase, kidney anion exchanger, chloride channel Clcka, carbonic anhydrase 2, aldolase) were co-regulated during acidosis. We propose that these trancripts cooperating to a same function and co-regulated during acidosis constitute a functional regulon. Keywords: SAGE; Kidney collecting duct; Mouse; Metabolic acidosis; V-ATPase
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