Comparison of oligonucleotide-microarray and serial analysis of gene expression (SAGE) in transcript profiling analysis of megakaryocytes derived from CD34+ cells.
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.
Kim
Hyung-Lae
HL
Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul, Korea. hyung@ewha.ac.kr
D018952:Antigens, CD34 / Q000378:metabolism*; D005312:Fetal Blood; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008533:Megakaryocytes / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000032:analysis / Q000235:genetics; D015203:Reproducibility of Results; D014158:Transcription, Genetic / Q000235:genetics*
D018952:Antigens, CD34; D012333:RNA, Messenger