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NRCD Human Full-Length cDNA Clone

NRCD Human Full-Length cDNA Clones

The RIKEN BioResource Center is distributing copies of full-length human cDNA clones that were produced by Dr. Seishi Kato of the Research Institute of National Rehabilitation Center for Persons with Disabilities to collect an entire set of full-length cDNA clones derived from human retina-derived cell lines. Approximately 39,000 clones corresponding to 7,067 genes are available.

Property of these libraries:
(1) The libraries containing sequences from their cap site to their poly(A) tail
Because cDNA produced from capped mRNA by the V-Capping Method has an additional dGMP (G) at its 5' end, we can validate full-length cDNA by the presence of an additional G at that terminal (Kato, S. et al., 2005).
(2) Few occasions of nucleotide substitution and deletion
Because the V-Capping Method lacks a PCR step and an amplification step, errors of nucleotide substitution and deletion produced in the steps are few occasions.
(3) The libraries containing cDNA derived from rare genes and long transcript
Because the V-Capping Method lacks a PCR step and an amplification step, gene expression levels and transcript size are no longer caveats in the making of cDNA libraries. These cDNA libraries constructed from ARPE-19 and Y79 cells contained many long (more than 7 kbp) cDNA clones (Kato, S. et al., 2005; Oshikawa, M. et al., 2008, 2011). The length of the longest cDNA was approximately 13 kbp (Oshikawa, M. et al., 2011).
(4) The libraries containing many variants of cDNA
Because gene expression levels and transcript size are no longer caveats in the making of cDNA libraries by the V-Capping Method, these libraries contain many variant cDNAs from the same gene locus by alternative promoter usage, diverse transcriptional initiation, alternative splicing, and alternative polyadenylation (Oshikawa, M. et al., 2008, 2011).
(5) The clones containing unidirectional cDNA as an insert fragment
The V-Capping Method enables us a unidirectional cDNA cloning, and the cDNAs for an antisense gene can be assured (Oshikawa, M. et al., 2008, 2011).

Source of RNA:
AR Library: human retinal pigment epithelium cell line, ARPE-19 (CRL-2302, ATCC)
RB Library: human retinoblastoma cell line, Y79 (HTB-18, ATCC)

Method of Generation of Full-Length cDNA:
Vector-Capping Method (V-Capping Method, Kato, S. et al., 2005, 2011)

Vector Backbone:
The following vectors derived from pKA1 (Kato, S. et al, 1994)
pKA1U5 (accession no. AB191256 (map), Kato, S. et al., 2005)
pGCAP1 (accession no. AB191257 (map), Kato, S. et al., 2005)
pGCAP10 (accession no. AB371573 (map), Oshikawa, M. et al., 2008)

Property of the 5' terminal region of full-length cDNA:
Boundary region of vectors (lower case) and full-length cDNA (capital letter) is indicated. One G (indicated by red character) is inserted between the vector sequence and 5' terminal of cDNA. In some case, some nucleotide (single or multiple T, or single G in many case) is inserted before G (Kato, S. et al., 2005). During synthesis of the first strand cDNA from vector primers, some nucleotide sequences were not removed well because of an insufficient digestion by restriction enzymes (Kato, S. et al., 2011). The NotI recognition site is placed downstream of poly(A) site.

pKA1U5 (EcoRI site is underlined):
...(vector)..tatagggaattccacccccctggtggat-G-GCTCT..(cDNA)...

pGCAP1 (EcoRI site is underlined):
...(vector)..tatagggaattccttaagattt-G-GCTCT..(cDNA)...

pGCAP10 (SwaI site is underlined):
...(vector)..tatagggaatttaaatgaatt-G-GCTCT..(cDNA)...

References:
The papers describing these libraries have been published in journals indicated below:

  1. Kato, S. Identification of genuine alternative splicing variants for rare or long-sized transcripts. In: DiMaggio S. and Braschipp E. eds. New Developments in Alternative Splicing Research. New York, Nova Biomedical. p.89-108, 2013.
    https://www.novapublishers.com/catalog/product_info.php?products_id=46700&osCsid=168c08748e890891d8335a0f23b338ea
  2. Oshikawa M, Tsutsui C, Ikegami T, Fuchida Y, Matsubara M, Toyama S, Usami R, Ohtoko K, Kato S. Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. Invest Ophthalmol Vis Sci. 52 (9), 6662-6670, 2011.
    http://www.iovs.org/content/52/9/6662.abstract
  3. Oshikawa M, Sugai Y, Usami R, Ohtoko K, Toyama S, Kato S. Fine expression profiling of full-length transcripts using a size-unbiased cDNA library prepared with the vector-capping method. DNA Res. 15 (3), 123-136, 2008.
    http://dnaresearch.oxfordjournals.org/content/15/3/123.long
  4. Kato S, Oshikawa M, Ohtoko K. Full-length transcriptome analysis using a bias-free cDNA library prepared with the vector-capping method. Methods Mol Biol. 729, 53-70, 2011.
    http://www.springerlink.com/content/v167171110r03558/#section=864398&page=1
  5. Kato S, Ohtoko K, Ohtake H, Kimura T. Vector-capping: a simple method for preparing a high-quality full-length cDNA library. DNA Res. 12 (1), 53-62, 2005.
    http://dnaresearch.oxfordjournals.org/content/12/1/53.long
  6. Kato, S., Sekine, S., Oh S., Kim, N., Umezawa, Y., Abe, N., Yokoyama-kobayashi, M., Aoki, T. Construction of human full-length cDNA bank. Gene 150, 243-250, 1994.
    http://www.sciencedirect.com/science/article/pii/0378111994904332

Information for the clones and vectors are available here.

Ordering NRCD Human Full-Length cDNA Clones

in Japanese

Terms and Conditions for Distribution:

  1. When publishing research results obtained by use of the BIOLOGICAL RESOURCE, please include acknowledgments to Dr. Seishi Kato the Research Institute of National Rehabilitation Center for Persons with Disabilities.
  2. The availability of the BIOLOGICAL RESOURCE is limited to a RECIPIENT of a not-for profit institution for a not-for-profit research. In any other cases, the RECIPIENT must obtain a prior written permission from the DEPOSITOR.
  3. When requested by the DEPOSITOR, RIKEN BRC informs the DEPOSITOR on the RECIPIENT's name, his/her affiliation and purpose of the use of clones.
    Uses other than for academic research by non-profit institutions:
    Please contact the Gene Engineering Division.

Form:
DNA solution with TE buffer (approx. 1 microgram) per clone.
Remarks:
♦ Terminal nucleotide sequences of cDNA are checked prior to delivery.
♦ Please allow 2 weeks before shipment.

If you have any questions regarding our DNA resources or related matters, please feel free to contact the Gene Engineering Division.

Clone search

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Download data file

Step 1. Searching HP ID (using Table 1)

  • Download Table 1.
  • Using the Table 1, please seek an HP ID of your concerning gene. Table 1 contains 7,067 genes in these library. HP ID is an identifier given by the Depositor.
  • According to the Entrez Gene Database of the NCBI, Gene Symbol, Gene ID, Protein Name, RefSeq accession number, length of mRNA, location on the human chromosome and UniGene ID are included in this table. Number of full-length clones in AR and RB libraries are also indicated.
Step 2. Searching Clone ID (using Table 2)
  • Download Table 2 (NRCDhumclone.xls).
  • Using Table 2, please seek clones with the HP ID obtained in Table 1. In many case, you may find two or more clones with the same HP ID.
  • In the Table 2, Clone ID, Name of Vector, Nucleotide Accession Number of DDBJ/EMBL/GenBank (if available) and 60 bp of 5' terminal sequence of the cDNA is included. The nucleotide sequence also contains additional G and a short fragment of vector (indicated with blue font in the Table 2) in some cases.

Order Forms and Material Transfer Agreement (MTA)

Obtain FormA.
  • Order Form and application of the payment by credit card.
    Click here for details.
  • Registration and downloading Order Form (Payment by Credit card).
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  • Order Form and application of the payment by bank transfer and check.
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Please complete the form with your shipping information including your account number of an international courier
(FedEx. World Courier, TNT Express, DHL Global Forwarding and others).

Forms Description Form Download
Form C Material Transfer Agreement We request a signature of an authorized representative of a recipient institution.
In the the Section 2(a), please write your purpose of use of clone in 10 to 20 words.
PDF: 90 KB

Address for orders

Please complete one copy of Form A and two copies of Form C and send them to the Gene Engineering Division by post or e-mail. In case sending them by e-mail, please send us the originals by post afterwards.
We look forward to receiving your order.

    Gene Engineering Division, RIKEN BioResource Center,
    3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
  • ♦ If you are not sure that you have completed forms correctly, please send them to us by e-mail or fax we will look them over.
    E-mail: dnabank@brc.riken.jp
    Fax: 029-836-9120

Payment and charges

An INVOICE will be sent to you once you have received the requested materials.
Please refer to the following page for more details:
http://dna.brc.riken.jp/en/furnish.html
RIKEN is a non-profit organization and therefore requires all applicants to cover all bank charges, (including exchange, commission and handling fees) incurred in sending payment for resources they have ordered.

Notice of Citations

    ♦ When publishing, in scientific journals, the results of research involving the use of materials from RIKEN BRC, please be sure to cite the paper designated by the depositor as well as to mention that these materials were provided by RIKEN BRC as follows: (name of BIOLOGICAL RESOURCE) was provided by the RIKEN BRC which is participating in the MEXT National BioResource Project (Japan).
To contact us:
  • Address: Gene Engineering Division, RIKEN BioResource Center,
    3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074 Japan
  • Fax: (+81)-29-836-9120
  • E-mail: dnabank@brc.riken.jp

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(T.M. 2011.07.25)

2017.02.04