Unknown,Transcriptomics,Genomics,Proteomics

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Global comparative transcriptome analysis of cartilage formation in vivo

ABSTRACT: We set out to characterize the gene expression changes which take place during chondrogenesis in the developing mouse limb. RNA derived from pre-condensed mesenchyme, mesenchymal condensations, and cartilage anlagen representing the earliest stages of tibial and fibular development was analysed by whole genome microarray analysis, and revealed 931 genes differentially expressed in these tissues. Among them were 892 genes not previously identified during the initation of chondrogenesis, including members of the Bmp, Wnt, Gdf, Sox, and Fox gene families. These microarray data were validated by qPCR, in situ hybridisation, and analysis of numerous genes already implicated in chondrogenesis in the scientific literature. 231 sections from a total of four 11.5dpc mouse hind limbs, three 12.5dpc mouse hind limbs, and four 13.5dpc mouse hind limbs (all from separate mice) were microdissected, and tissues from each time point were pooled. Thus, this experiment consisted of one replicate only.

ORGANISM(S): Mus musculus

SUBMITTER: Trevor Cameron

PROVIDER: E-GEOD-35669 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Global comparative transcriptome analysis of cartilage formation in vivo.

Cameron Trevor L TL Belluoccio Daniele D Farlie Peter G PG Brachvogel Bent B Bateman John F JF

BMC developmental biology 20090310

<h4>Background</h4>During vertebrate embryogenesis the initial stages of bone formation by endochondral ossification involve the aggregation and proliferation of mesenchymal cells into condensations. Continued growth of the condensations and differentiation of the mesenchymal cells into chondrocytes results in the formation of cartilage templates, or anlagen, which prefigure the shape of the future bones. The chondrocytes in the anlagen further differentiate by undergoing a complex sequence of m ...[more]

PMID: 19272164

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Project description:Detailed information about stage-specific changes in gene expression is crucial for understanding the gene regulatory networks underlying development and the various signal transduction pathways contributing to morphogenesis. Here, we describe the global gene expression dynamics during early murine limb development, when cartilage, tendons, muscle, joints, vasculature, and nerves are specified and the musculoskeletal system of the limbs is established. We used whole-genome microarrays to identify genes with differential expression at 5 stages of limb development (E9.5 to 13.5), during fore-limb and hind-limb patterning. We found that the onset of limb formation is characterized by an up-regulation of transcription factors, which is followed by a massive activation of genes during E10.5 and E11.5 which tampers off at later time points. Among 3520 genes identified as significantly up-regulated in the limb, we find ~30% to be novel, dramatically expanding the repertoire of candidate genes likely to function in the limb. Hierarchical and stage-specific clustering identified expression profiles that correlate with functional programs during limb development and are likely to provide new insights into specific tissue patterning processes. Here we provide for the first time, a comprehensve analysis of developmentally regulated genes during murine limb development, and provide some novel insights into the expression dynamics governing limb morphogenesis. Fifty- one arrays were analyzed, consisting of whole fore-limb and hind-limb bud RNA (experimental) and whole embryo RNA (reference) samples from E9.5 to E13.5 DPC mouse (FVB strain). Embryos were not pooled to generate samples. Each time point has 3 to 5 biological replicates for limb bud samples, duplicates for whole embryos. Comparisons were made between limb bud samples and whole embryo at the same stage, fore-limb samples of different stages, hind-limb samples of different stages, and fore-limb samples compared to hind-limb samples at the same or the next stage.

Dataset Information

Global comparative transcriptome analysis of cartilage formation in vivo

Publications

Global comparative transcriptome analysis of cartilage formation in vivo.

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