Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

SADE analysis of microdissected kidney

ABSTRACT: Libraries generated from microdissected kidney samples from the healthy pole of cancerous kidneys. Donors were from either sex. Libraries were generated using Sau3A I as anchoring enzyme. Data are provided after removal of linker derived sequences. Keywords: other

ORGANISM(S): Homo sapiens

SUBMITTER: Jean-Marc Elalouf

PROVIDER: E-GEOD-694 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A panoramic view of gene expression in the human kidney.

Chabardès-Garonne Danielle D Mejéan Arnaud A Aude Jean-Christophe JC Cheval Lydie L Di Stefano Antonio A Gaillard Marie-Claude MC Imbert-Teboul Martine M Wittner Monika M Balian Chanth C Anthouard Véronique V Robert Catherine C Ségurens Beatrice B Wincker Patrick P Weissenbach Jean J Doucet Alain A Elalouf Jean-Marc JM

Proceedings of the National Academy of Sciences of the United States of America 20031031 23

To gain a molecular understanding of kidney functions, we established a high-resolution map of gene expression patterns in the human kidney. The glomerulus and seven different nephron segments were isolated by microdissection from fresh tissue specimens, and their transcriptome was characterized by using the serial analysis of gene expression (SAGE) method. More than 400,000 mRNA SAGE tags were sequenced, making it possible to detect in each structure transcripts present at 18 copies per cell wi ...[more]

PMID: 14595018

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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 Approximately 650 OMCDs were microdissected, as previously described from collagenase-treated kidneys of 6 mice fed the NH4Cl-supplemented diet for 3 days. 20960 tags were sequenced in the acidosis SAGE library. After withdrawing duplicate ditags and linker sequences, the 19146 tags remaining corresponded to 8847 different tags.This acidosis library is similar in size and diversity to the normal mouse OMCD libraries previously generated (GEO accession number : GSM23478). The tag abundance in the two library was compared and discussed.

Dataset Information

SADE analysis of microdissected kidney

Publications

A panoramic view of gene expression in the human kidney.

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