Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of Xenopus pronephric explants in presence or absence of hedgehog

ABSTRACT: Pronephric explants were dissected in the presence or absence of hedgehog signaling. Targets from pooled biological samples were examined in triplicate and the expression profiles were determined using Affymetrix Xenopus Genechip 1 arrays. Experiment Overall Design: 3 bhh treated pooled explants and 3 untreated pooled explants were analyzed

ORGANISM(S): Xenopus laevis

SUBMITTER: Curtis Altmann

PROVIDER: E-GEOD-3712 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

FGF is essential for both condensation and mesenchymal-epithelial transition stages of pronephric kidney tubule development.

Urban Anna E AE Zhou Xiaolan X Ungos Josette M JM Raible David W DW Altmann Curtis R CR Vize Peter D PD

Developmental biology 20060505 1

The pronephros is a transient embryonic kidney that is essential for the survival of aquatic larvae. It is also absolutely critical for adult kidney development, as the pronephric derivative the wolffian duct forms the ductal system of the adult kidney and also triggers the condensation of metanephric mesenchyme into the adult nephrons. While exploring Xenopus pronephric patterning, we observed that epidermally delivered hedgehog completely suppresses pronephric kidney tubule development but doe ...[more]

PMID: 16872594

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Project description:In Cichorium intybus, macroscopic and histological modifications were identified during in vitro cell reactivation and morphogenesis events. The relationships between these modifications and transcript profiles of genes were investigated. Two chicory genotypes derived from the Hungarian landrace Koospol, were tested: K59 is a responsive genotype (embryogenic), as it undergoes cell de- and re-differentiation that leads to somatic embryogenesis (SE). C15 is an unresponsive genotype (nonembryogenic), unable to express this morphogenetic pattern. Previously studies showed that addition of beta-D-glucosyl Yariv reagent (BGlcY), a synthetic phenyl-glycoside that specifically binds arabinogalactan-proteins (AGPs), to the culture medium blocked somatic embryogenesis in chicory root explants in a concentration-dependent manner with complete inhibition of induction occurring at 250 ÂµM of BGlcY (Chapmann et al. 2000a). A putative AGP (DT212818) encoding gene was previously found significantly over-expressed in the K59 as compared to the C15 and was suggested to be involved in chicory re-differentiation. To better understand the cell reactivation events, a treatment with BGlcY was applied in order to precipitate AGPs in muro and to block the in vitro cell re-differentiation processes. The two different genotypes together with BGlcY represented an original tool to discriminate cell reactivation events from cell fate determination. Microscopy, biochemical and transcriptome analyses showed that in vitro SE in chicory was blocked during BGlcY-treatment but cell reactivation still occurred. Consequently, AGP (DT212818) seems to be only important in cell fate determination leading to SE commitment. Gene expression profiles showed in addition to the AGP, other proteins could play a role in SE determination: 26S proteasome AAA ATPase subunit 6 (RPT6), remorin (REM), metallothionein 1 (MT1), 3-hydroxy-3-methylglutaryl-CoA reductase (HMG-CoA reductase). Cell wall events during BGlcY-treatment were observed and discussed. Gene expression of K59 explants induced (d4) was compared with gene expression of K59 explants without induction (d0). Gene expression of K59 explants induced in the presence of BGlcY (Y+; d4) was next compared with gene expression of K59 explants induced in the absence of BGlcY (Y-; d4). Similar comparisons were made for C15 leaf explants. To link up both genotypes, direct comparison was done between gene expression of K59 explants without induction (d0) and C15 explants without induction (d0). Three biological replicates were used for each analysed condition. Dye labelling for each paired sample was reversed in two subsequent individual hybridizations giving rise to a total of six hybridizations per condition except for the K59_D0_vs_C15_D0 condition.

Dataset Information

Transcription profiling of Xenopus pronephric explants in presence or absence of hedgehog

Publications

FGF is essential for both condensation and mesenchymal-epithelial transition stages of pronephric kidney tubule development.

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