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Fine Expression Profiling of Full-length Transcripts using a Size-unbiased cDNA Library Prepared with the Vector-capping Method

Recently, we have developed a vector-capping method for constructing a full-length cDNA library. In the present study, we performed in-depth analysis of the vector-capped cDNA library prepared from a single type of cell. As a result of single-pass sequencing analysis of 24 000 clones randomly isolat...

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Detalles Bibliográficos
Autores principales: Oshikawa, Mio, Sugai, Yoshiko, Usami, Ron, Ohtoko, Kuniyo, Toyama, Shigeru, Kato, Seishi
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2650634/
https://www.ncbi.nlm.nih.gov/pubmed/18487259
http://dx.doi.org/10.1093/dnares/dsn010
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author Oshikawa, Mio
Sugai, Yoshiko
Usami, Ron
Ohtoko, Kuniyo
Toyama, Shigeru
Kato, Seishi
author_facet Oshikawa, Mio
Sugai, Yoshiko
Usami, Ron
Ohtoko, Kuniyo
Toyama, Shigeru
Kato, Seishi
author_sort Oshikawa, Mio
collection PubMed
description Recently, we have developed a vector-capping method for constructing a full-length cDNA library. In the present study, we performed in-depth analysis of the vector-capped cDNA library prepared from a single type of cell. As a result of single-pass sequencing analysis of 24 000 clones randomly isolated from the unamplified library, we identified 19 951 full-length cDNA clones whose intactness was confirmed by the presence of an additional G at their 5' end. The full-length cDNA content was >95%. Mapping these sequences to the human genome, we identified 4513 transcriptional units that include 36 antisense transcripts against known genes. Comparison of the frequencies of abundant clones showed that the expression profiles of different libraries, including the distribution of transcriptional start sites (TSSs), were reproducible. The analysis of long-sized cDNAs showed that this library contained many cDNAs with a long-sized insert up to 11 199 bp of golgin B, including multiple slicing variants for filamin A and filamin B. These results suggest that the size-unbiased full-length cDNA library constructed using the vector-capping method will be an ideal resource for fine expression profiling of transcriptional variants with alternative TSSs and alternative splicing.
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spelling pubmed-26506342009-04-13 Fine Expression Profiling of Full-length Transcripts using a Size-unbiased cDNA Library Prepared with the Vector-capping Method Oshikawa, Mio Sugai, Yoshiko Usami, Ron Ohtoko, Kuniyo Toyama, Shigeru Kato, Seishi DNA Res Full Papers Recently, we have developed a vector-capping method for constructing a full-length cDNA library. In the present study, we performed in-depth analysis of the vector-capped cDNA library prepared from a single type of cell. As a result of single-pass sequencing analysis of 24 000 clones randomly isolated from the unamplified library, we identified 19 951 full-length cDNA clones whose intactness was confirmed by the presence of an additional G at their 5' end. The full-length cDNA content was >95%. Mapping these sequences to the human genome, we identified 4513 transcriptional units that include 36 antisense transcripts against known genes. Comparison of the frequencies of abundant clones showed that the expression profiles of different libraries, including the distribution of transcriptional start sites (TSSs), were reproducible. The analysis of long-sized cDNAs showed that this library contained many cDNAs with a long-sized insert up to 11 199 bp of golgin B, including multiple slicing variants for filamin A and filamin B. These results suggest that the size-unbiased full-length cDNA library constructed using the vector-capping method will be an ideal resource for fine expression profiling of transcriptional variants with alternative TSSs and alternative splicing. Oxford University Press 2008-06 2008-05-16 /pmc/articles/PMC2650634/ /pubmed/18487259 http://dx.doi.org/10.1093/dnares/dsn010 Text en © The Author 2008. Kazusa DNA Research Institute
spellingShingle Full Papers
Oshikawa, Mio
Sugai, Yoshiko
Usami, Ron
Ohtoko, Kuniyo
Toyama, Shigeru
Kato, Seishi
Fine Expression Profiling of Full-length Transcripts using a Size-unbiased cDNA Library Prepared with the Vector-capping Method
title Fine Expression Profiling of Full-length Transcripts using a Size-unbiased cDNA Library Prepared with the Vector-capping Method
title_full Fine Expression Profiling of Full-length Transcripts using a Size-unbiased cDNA Library Prepared with the Vector-capping Method
title_fullStr Fine Expression Profiling of Full-length Transcripts using a Size-unbiased cDNA Library Prepared with the Vector-capping Method
title_full_unstemmed Fine Expression Profiling of Full-length Transcripts using a Size-unbiased cDNA Library Prepared with the Vector-capping Method
title_short Fine Expression Profiling of Full-length Transcripts using a Size-unbiased cDNA Library Prepared with the Vector-capping Method
title_sort fine expression profiling of full-length transcripts using a size-unbiased cdna library prepared with the vector-capping method
topic Full Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2650634/
https://www.ncbi.nlm.nih.gov/pubmed/18487259
http://dx.doi.org/10.1093/dnares/dsn010
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