Transcriptomics

Dataset Information

22

Transcriptional profiling of equine chondrocyte de-differentiation in culture


ABSTRACT: Monolayer cultures of primary chondrocytes undergo morphological changes that have been broadly characterized as de-differentiation. Transcriptional profiling was used to evaluate changes in gene expression during this process. Articular cartilage was harvested from a single Standardbred horse; the chondrocytes were isolated and then maintained in monolayer culture for up to 14 days. Chondrocytes were collected on Day 1 and Day 14 of culture and snap frozen in liquid nitrogen. Total RNA was isolated, subjected to one round of linear RNA amplification, and then applied to an equine-specific cDNA microarray composed of 9322 elements. Three biological replicates were analyzed at each time point using a dye-swap experimental design. One hundred six transcripts were present at levels greater than or equal to five-fold higher in Day 1 chondrocytes relative to the cells collected at Day 14. Conversely, 68 transcripts were present at levels greater than or equal to five-fold higher in Day 14 chondrocytes. Northern blot hybridization validated the microarray data by confirming the down-regulation of steady state mRNA levels for type II procollagen and aggrecan core protein and the up-regulation of type I procollagen. Gene-by-gene and cluster analyses will be used to compare the process of “de-differentiation” in primary culture to the developmental stages of normal chondrocyte differentiation and to the fibrocartilage repair tissue that forms in osteoarthritic lesions. Keywords: articular cartilage, de-differentiation, horse, cDNA microarray Overall design: This is a direct comparison between one and fourteen day cultured chondrocyte transcriptomes. Three sets of technical replicates were compared. For each comparison and its dye-swap, one Day 1 technical replicate was randomly compared to one Day 14 technical replicate.

INSTRUMENT(S): MacLeod custom equine cartilage cDNA microarray

ORGANISM(S): Equus caballus  

SUBMITTER: Michael J. Mienaltowski  

PROVIDER: GSE14255 | GEO | 2012-06-01

SECONDARY ACCESSION(S): PRJNA111209

REPOSITORIES: GEO

Similar Datasets

2012-05-31 | E-GEOD-14255 | ArrayExpress
2008-11-10 | GSE10303 | GEO
2012-11-14 | E-GEOD-42235 | ArrayExpress
2010-03-30 | GSE14252 | GEO
| GSE104793 | GEO
| GSE104795 | GEO
| GSE104794 | GEO
2009-09-02 | GSE16464 | GEO
2009-09-13 | E-GEOD-16464 | ArrayExpress
2013-12-16 | E-GEOD-51812 | ArrayExpress