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

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

10.1101/gr.145100

Crossref journal-article

Cold Spring Harbor Laboratory

Genome Research (246)

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.

Bibliography

Carninci, P., Shibata, Y., Hayatsu, N., Sugahara, Y., Shibata, K., Itoh, M., Konno, H., Okazaki, Y., Muramatsu, M., & Hayashizaki, Y. (2000). Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes. Genome Research, 10(10), 1617â1630.

Authors 10

Piero Carninci (first)
Yuko Shibata (additional)
Norihito Hayatsu (additional)
Yuichi Sugahara (additional)
Kazuhiro Shibata (additional)
Masayoshi Itoh (additional)
Hideaki Konno (additional)
Yasushi Okazaki (additional)
Masami Muramatsu (additional)
Yoshihide Hayashizaki (additional)

References 25 Referenced 228

10.1126/science.2047873
{'key': '2021111810350424000_10.10.1617.2', 'first-page': '3', 'article-title': 'Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides cDNA sequence.', 'volume': '377:(Suppl.)', 'author': 'Adams', 'year': '1995', 'journal-title': 'Nature'} / Nature / Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides cDNA sequence. by Adams (1995)
Anderson M. Young B.D. (1985) Quantitative analysis of solution hybridisation. Nucleic Acids Hybridisation, a practical approach (IRL Press, Oxford), pp 73–111.
10.1016/0003-2697(90)90096-R
10.1101/gr.6.9.791
10.1016/S0076-6879(99)03004-9 / Methods Enzymol. / High-efficiency full-length cDNA cloning. by Carninci (1999)
10.1073/pnas.95.2.520
10.1006/geno.1996.0567
10.1073/pnas.93.12.6025
10.1128/MCB.15.6.3363 / Mol. Cell Biol. / An efficient strategy to isolate full-length cDNAs based on an mRNA cap retention procedure (CAPture). by Edery (1995)
10.1016/0003-2697(90)90471-K
10.1101/gr.6.9.807
10.1038/ng0595-77
10.1016/0378-1119(94)90433-2
10.1093/nar/25.6.1315
10.1101/gr.9.5.463 / Genome Res. / Automated filtration-based high-throughput plasmid preparation system. by Itoh (1999)
10.1038/5976
10.1016/0378-1119(94)90802-8
10.1126/science.287.5461.2222
Sambrook J. Fritsch E. Maniatis T. (1989) Molecular Cloning. (Cold Spring Harbor laboratory press, Cold Spring Harbor, NY).
10.1093/nar/22.6.987
10.1006/geno.1998.5209
10.1073/pnas.91.20.9228
10.1006/geno.1994.1478
10.1006/geno.1996.0344

Dates

Type	When
Created	23 years, 1 month ago (July 26, 2002, 8 p.m.)
Deposited	3 years, 9 months ago (Nov. 18, 2021, 1:52 p.m.)
Indexed	4 weeks ago (Aug. 5, 2025, 8:31 a.m.)
Issued	24 years, 11 months ago (Oct. 1, 2000)
Published	24 years, 11 months ago (Oct. 1, 2000)
Published Online	24 years, 11 months ago (Oct. 1, 2000)
Published Print	24 years, 11 months ago (Oct. 1, 2000)

Funders 0

None

BibTeX

@article{Carninci_2000, title={Normalization and Subtraction of Cap-Trapper-Selected cDNAs to Prepare Full-Length cDNA Libraries for Rapid Discovery of New Genes}, volume={10}, ISSN={1549-5469}, url={http://dx.doi.org/10.1101/gr.145100}, DOI={10.1101/gr.145100}, number={10}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory}, author={Carninci, Piero and Shibata, Yuko and Hayatsu, Norihito and Sugahara, Yuichi and Shibata, Kazuhiro and Itoh, Masayoshi and Konno, Hideaki and Okazaki, Yasushi and Muramatsu, Masami and Hayashizaki, Yoshihide}, year={2000}, month=oct, pages={1617–1630} }

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