Comparison of oligonucleotide-microarray and serial analysis of gene expression (SAGE) in transcript profiling analysis of megakaryocytes derived from CD34+ cells.
- Author:
Hyung Lae KIM
1
Author Information
1. Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul, Korea.
- Publication Type:Original Article ; Comparative Study ; Research Support, Non-U.S. Gov't
- MeSH:
Antigens, CD34/*metabolism;
Comparative Study;
Fetal Blood;
Gene Expression Profiling/*methods;
Human;
Megakaryocytes/*metabolism;
Oligonucleotide Array Sequence Analysis/*methods;
RNA, Messenger/analysis/genetics;
Reproducibility of Results;
Support, Non-U.S. Gov't;
Transcription, Genetic/*genetics
- From:Experimental & Molecular Medicine
2003;35(5):460-466
- CountryRepublic of Korea
- Language:English
-
Abstract:
For the comprehensive analysis of transcript expression, the array-based hybridization analysis and the serial analysis of gene expression (SAGE) are commonly used platforms. The SAGE is based on a high-throughput sequencing of ditags derived from the transcript. DNA microarrays are a powerful tool for monitoring thousands of transcripts simultaneously, whereas the Genechip (Affimatrix microarray) technology is based on the hybridization of a single probe or other manufacturer's microarrays (cDNA- or oligonucleotide-microarray) procedures include the competitive hybridization of two probes. In this study, the quantitative accuracy of expression using oligonucleotide-microarray was determined by comparing data set from the SAGE. In previous study the microSAGE was performed for the megakaryocytes and non- megakaryocytes derived from human cord blood CD34(+)cells by ex vivo expansion using thrombopoietin, and a total of 38,909 tags representing 8,976 unique genes were obtained. On the identical RNA, expression profiling was also carried out using oligonucleotide-microarray (MAGIC II 10K chip, Macrogen). The most frequently expressed genes in human megakaryocytes were identified as platelet factor 1 followed by annexin A1, ribosomal protein S23. The majority of the 50 most highly expressed genes in the CD34(+)-derived megakaryocytes were those involved in protein synthesis, e.g., ribosomal proteins. The expression level through the single channel of oligonucleotide-microarray and SAGE have a fairly good correlation in terms of absolute analyses and that the correlation is higher for the genes with higher expression levels.
