Transcriptional profiling of growth plate chondrocyte differentiation yields insight into endochondral ossification
From ArrayWiki
| PubMed ID: | none |
|---|---|
| Contact: | Claudine James
|
| Species: | Mus musculus |
| Platform: | Affymetrix GeneChip Mouse Genome 430 2.0 Array |
| Number of Samples: | 12 |
| Date Range: | 07/07/2006 - 07/07/2006 |
| Experiment Quality: | UF: 94.69 AC: 0.82 % 96.94 |
| Link to Repository: | GSE7685 |
| Original Intensity Data: | Download |
| Clean Intensity Data: | Download |
| Original PLIER Data: | Download |
| Clean PLIER Data: | Download |
| Clean CEL Files: | Download |
| Data Rank: | 
|
A variety of cell cultures models and in vivo approaches have been used to study gene expression during chondrocyte differentiation. The extent to which the in vitro models reflect bona fide gene regulation in the growth plate has not been quantified. In addition, studies that evaluate global gene expression changes among different growth plate zones are limited. To address these issues, we completed a microarray screen of three growth plate zones derived from manually segmented embryonic mouse tibiae. Classification of genes differentially expressed between each respective growth plate zone, functional categorization as well as characterization of gene expression patterns, cytogenetic loci, signaling pathways and functional motifs confirmed documented data and pointed to novel aspects of chondrocyte differentiation. Parallel comparisons of the microdissected tibiae data set to our previously completed micromass culture screen further corroborated the suitability of micromass cultures for modeling gene expression in chondrocyte development. The micromass culture system demonstrated striking similarities to the in vivo microdissected tibiae screen; however, the micromass system was unable to accurately distinguish gene expression differences in the hypertrophic and mineralized zones of the growth plate. These studies will allow us to better understand zone-specific gene expression patterns in the growth plate. Ultimately, this work will help define both the genomic context in which genes are expressed in the long bones and the extent to which the micromass culture system is able to recapitulate chondrocyte development in endochondral ossification.
Design: Array
Type: Growth plate microdissection
Contents |
[edit] Contributors
- Lee-Anne Stanton
- Hanga Agoston
- Claudine G James
- T M Underhill
- Frank Beier
[edit] Protocols
[edit] References
[edit] Links
GEO Accession for this experiment: GSE7685. (Public on Sep 01 2007)
RAW data: tar file.
[edit] Analysis
 Before Normalization |
 After Normalization & Cleaning |
[edit] Samples/Quality Control
| Sample | Date Scanned | Source Link | Probe Variance Data | Artifact Mask | Quality Score |
|---|---|---|---|---|---|
| II-A | 07/07/06 12:20:00 | GSM186191 | 
| 
| UF: 93.4135 AC: 0.66 % 96.38 |
| III-A | 07/07/06 13:18:52 | GSM186192 | 
| 
| UF: 94.6099 AC: 0.08 % 96.26 |
| I-B | 07/07/06 11:57:49 | GSM186193 | 
| 
| UF: 93.5099 AC: 1.04 % 96.23 |
| II-B | 07/07/06 14:18:50 | GSM186194 | 
| 
| UF: 95.305 AC: 1.37 % 96.94 |
| III-B | 07/07/06 13:41:05 | GSM186195 | 
| 
| UF: 94.0398 AC: 0.08 % 96.97 |
| I-C | 07/07/06 13:59:51 | GSM186196 | 
| 
| UF: 95.9846 AC: 3.5 % 96.24 |
| II-C | 07/07/06 13:30:06 | GSM186197 | 
| 
| UF: 93.4709 AC: 2.05 % 95.71 |
| III-C | 07/07/06 15:21:06 | GSM186198 | 
| 
| UF: 95.0183 AC: 0.03 % 97.49 |
| I-D | 07/07/06 15:32:53 | GSM186199 | 
| 
| UF: 95.5043 AC: 0.11 % 97.70 |
| II-D | 07/07/06 15:44:46 | GSM186200 | 
| 
| UF: 95.5815 AC: 0.17 % 97.71 |
| III-D | 07/07/06 15:07:23 | GSM186201 | 
| 
| UF: 95.3688 AC: 0.21 % 97.58 |
| I-A | 07/07/06 12:08:46 | GSM186202 | 
| 
| UF: 94.4659 AC: 0.52 % 96.97 |
