Microarray hybridization with fractionated cDNA: enhanced identification of differentially expressed genes.
Molecular indexing is a technique to select a subpopulation of cDNA by ligation of adapters to cDNA fragments digested by a class IIS restriction enzyme(s). By this technique, 3' end cDNA fragments are divided into 16 fractions by selective ligation of adapters and subsequent PCR amplification. Each fraction is used as a hybridization target for microarray hybridization. This fractionated target has a relatively lower nucleic acid complexity, including more fractions for rare transcripts, and is useful for their detection. In an experiment with mouse cerebellum and cerebrum RNA, analysis of a subset of candidate genes indicated that 10 times more differentially expressed genes were detected by this method than by the conventional method using the unfractionated target.
Sakai
K
K
Taisho Laboratory of Functional Genomics, Nara Institute of Science and Technology, CREST, JST, 8916-5 Takayama, Ikoma, Nara, 630-0101, Japan.
Higuchi
H
H
Matsubara
K
K
Kato
K
K
D000818:Animals; D015152:Blotting, Northern; D002531:Cerebellum / Q000378:metabolism; D005591:Chemical Fractionation; D003001:Cloning, Molecular / Q000379:methods; D011088:DNA Ligases; D017931:DNA Primers / Q000737:chemistry; D018076:DNA, Complementary / Q000032:analysis / Q000235:genetics*; D005456:Fluorescent Dyes; D020869:Gene Expression Profiling / Q000379:methods*; D006824:Hybridization, Genetic / Q000235:genetics*; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009841:Oligonucleotides / Q000235:genetics; D016133:Polymerase Chain Reaction; D012333:RNA, Messenger / Q000032:analysis; D012680:Sensitivity and Specificity; D013687:Telencephalon / Q000378:metabolism; D014158:Transcription, Genetic
D017931:DNA Primers; D018076:DNA, Complementary; D005456:Fluorescent Dyes; D009841:Oligonucleotides; D012333:RNA, Messenger; D011088:DNA Ligases