Serial analysis of gene expression in murine fetal thymocyte cell lines.
FTL-1, -3 and -10 are three murine day 14 fetal thymocyte cell lines produced in order to model developmental stages within early (CD3-CD4-CD8-) thymocyte differentiation. In this study, we used the serial analysis of gene expression (SAGE) method to perform a systematic analysis of transcripts present in these three cell lines. A total of 77,313 SAGE tags were sequence identified from the three cell lines, representing 24,645 unique transcripts. Differentially expressed mRNA transcripts representing different gene classes were identified, including T cell functional genes, cytokine receptors, adhesion molecules and transcription factors. These results may serve as a model of the transcriptome of early thymocyte differentiation. A large number of unknown expressed sequence tags were also found to be differentially expressed. In order to validate the SAGE data, selected differentially expressed transcripts identified by SAGE were analyzed by quantitative RT-PCR in normal murine double-negative stage DN1-4 thymocytes. Expression of the transcription factors RUNX2 and PHD finger protein 2 and of the IGF type 1 receptor was shown to have differentially regulated expression patterns in sorted DN1-4 cells. These genes, and others identified by this analysis, are likely to play important roles in the development of T cells.
Zhao
Feng-Qi
FQ
Molecular Pathology Division, Department of Cellular Pathology and Genetics, Armed Forces Institute of Pathology, Rockville, MD 20850, USA.
Sheng
Zong-Mei
ZM
Tsai
Mark M
MM
Hubbs
Alan E
AE
Wang
Ruixue
R
O'Leary
Timothy J
TJ
Izon
David J
DJ
Taubenberger
Jeffery K
JK
D000818:Animals; D001483:Base Sequence; D002460:Cell Line; D019070:Cell Lineage; D050659:Core Binding Factor Alpha 1 Subunit; D004268:DNA-Binding Proteins / Q000235:genetics; D005333:Fetus / Q000166:cytology / Q000378:metabolism*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D064799:Hypoxia-Inducible Factor-Proline Dioxygenases; D017874:Immediate-Early Proteins; D051379:Mice; D008969:Molecular Sequence Data; D009363:Neoplasm Proteins; D011393:Procollagen-Proline Dioxygenase; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017526:Receptor, IGF Type 1 / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013950:Thymus Gland / Q000166:cytology / Q000196:embryology* / Q000378:metabolism*; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics
D050659:Core Binding Factor Alpha 1 Subunit; D004268:DNA-Binding Proteins; D017874:Immediate-Early Proteins; D009363:Neoplasm Proteins; D012333:RNA, Messenger; D014157:Transcription Factors; D011393:Procollagen-Proline Dioxygenase; C490189:Egln1 protein, mouse; D064799:Hypoxia-Inducible Factor-Proline Dioxygenases; D017526:Receptor, IGF Type 1