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Title: Atlas of gene expression in the mouse kidney      
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available
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instance of dataset
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refinement:
curated
dateReleased:
11-27-2011
ID:
E-GEOD-25223
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.
keywords:
transcription profiling by SAGE
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Array Express
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accessURL: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-25223
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JSON
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OmicsDI
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accessType:
download
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accessURL: www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-25223.json
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XML
storedIn:
OmicsDI
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accessType:
download
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accessURL: http://www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-25223.xml
ID:
SCR:014747
name:
Omics Discovery Index
abbreviation:
OmicsDI
homePage: http://www.omicsdi.org/