Gene expression profile of human chondrocyte HCS-2/8 cell line by EST sequencing analysis

Youn Kwan Jung, Jae Hwan Jeong, Hyun Mo Ryoo, Hyun Nam Kim, Yeon Ju Kim, Eui Kyun Park, Hyun Jung Si, Shin Yoon Kim, Masaharu Takigawa, Byung Hun Lee, Rang Woon Park, In San Kim, Je Yong Choi

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Large-scale single-pass sequencing of randomly selected cDNA clones from cell type specific libraries has proven to be a powerful approach for the discovery of novel gene functions, identification of novel gene family members, and definition of gene expression profiles. HCS-2/8 chondrocyte has been used as a cell culture model to study chondrocyte differentiation. Here we performed 3350 single-pass sequencing reactions obtained from the 5′ ends of cDNAs from HCS-2/8 cells. To define the expression profiles of HCS-2/8 chondrocytes, we analyzed the identity of these representative cDNA sequences using database searches (BLAST). The sequences represent 1927 unique genes with known function (i.e., unigene clusters), 38 transcripts that are similar to genes with known function, 739 expressed genes with unknown function (i.e., expressed sequence tags), and 18 cDNAs which have not previously been sequenced. Interestingly, many transcripts were expressed from chromosome 12 compared with total genes, while the fewer numbers of cDNAs were derived from genes on chromosomes 14, 18 and Y. The chondrocytic phenotype of HCS-2/8 cells is reflected by abundant expression of genes related to cell structure and motility and the 20 most frequently expressed unigenes reflect a chondrocyte-related gene expression signature. Thus, our data establish a representative set of more than 2000 genes expressed in a chondrocytic cell line. This finding provides a framework for understanding cell growth and differentiation of chondrocytes and their metabolic function in the formation and remodeling of cartilage.

Original languageEnglish
Pages (from-to)85-92
Number of pages8
JournalGene
Volume330
Issue number1-2
DOIs
Publication statusPublished - Apr 14 2004

Keywords

  • BLAST
  • Chondrocyte
  • Complementary DNA
  • EST
  • Expressed sequence tag
  • Expressed sequence tags
  • NCBI
  • National center for biotechnology information
  • Sequencing
  • cDNA
  • cDNA library

ASJC Scopus subject areas

  • Genetics

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