Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes

Piero Carninci; Yuko Shibata; Norihito Hayatsu; Yuichi Sugahara; Kazuhiro Shibata; Masayoshi Itoh; Hideaki Konno; Yasushi Okazaki; Masami Muramatsu; Yoshihide Hayashizaki

doi:10.1101/gr.145100

Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes

Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC) and Genome Science Laboratory, RIKEN Tsukuba Institute, Core Research of Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Tsukuba 305-0074, Japan

Abstract

In the effort to prepare the mouse full-length cDNA encyclopedia, we previously developed several techniques to prepare and select full-length cDNAs. To increase the number of different cDNAs, we introduce here a strategy to prepare normalized and subtracted cDNA libraries in a single step. The method is based on hybridization of the first-strand, full-length cDNA with several RNA drivers, including starting mRNA as the normalizing driver and run-off transcripts from minilibraries containing highly expressed genes, rearrayed clones, and previously sequenced cDNAs as subtracting drivers. Our method keeps the proportion of full-length cDNAs in the subtracted/normalized library high. Moreover, our method dramatically enhances the discovery of new genes as compared to results obtained by using standard, full-length cDNA libraries. This procedure can be extended to the preparation of full-length cDNA encyclopedias from other organisms.

Footnotes

↵1 Corresponding author.
E-MAIL rgscerg{at}rtc.riken.go.jp or carninci{at}rtc.riken.go.jp; FAX 81-298-369098.
Article and publication are at www.genome.org/cgi/doi/10.1101/gr.145100.
- Received April 20, 2000.
- Accepted July 24, 2000.
Cold Spring Harbor Laboratory Press