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Clontech Laboratories, Inc. and RIKEN BioResource Research Center concluded license agreement on preservation and distribution of Fluorescent Proteins, DsRed2 and mCherry for academic use

BRC News

NRCD Human cDNA Clone


The RIKEN BRC 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 7,000 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.
  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.
  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.
  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.
  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.
  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.

Please visit Informaion site for articles published by using this materials, references and tips.


Ordering NRCD Human Full-Length cDNA Clones

Terms and Conditions for Distribution:

    1. In publishing the research results to be obtained by use of the BIOLOGICAL RESOURCE, RECIPIENT must state an acknowledgment “This BIOLOGICAL RESOURCE deposited by Seishi Kato, Research Institute of National Rehabilitation Center for Persons with Disabilities, was provided by the RIKEN BRC.”.
    2. When requested by the DEPOSITOR, RIKEN BRC informs the DEPOSITOR on the name of resource, RECIPIENT’s name, his/her affiliation and purpose of the use.

 

Distribution fee per clone:
8,440 YEN (For use in research for not-for-profit academic purpose).
16,880 YEN (For use in research for-profit-research purpose).
(Shipping cost is not included.)

For details for fee and payment, please visit Information of Request for Distribution.
The distribution fee was revised from October 1, 2019

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.

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Order Forms and Material Transfer Agreement (MTA)

Order Form:
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).
See detail in Information of Request for Distribution

Note:
The resident of the European Economic Area (EEA) and China, please read Special distribution Information to Residents of the Foreign Countries
For Credit Card Payment. (Visa or Master Card only)
Order Form (Credit Card Payment) 
For bank transfer or check payment.
Order Form (Bank Transfer or Check Payment) 
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.

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.

The DNA Bank, RIKEN BioResource Research Center,
3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
E-mail: dnabank.brc@riken.jp
FAX: (+81)-29-836-9120

 

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: Information of Request for Distribution
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: The NRCD Human Full-Length cDNA clone was provided by the RIKEN BRC through the National BioResource Project of the MEXT/AMED, Japan.

To contact us:

The DNA Bank, RIKEN BioResource Research Center,
3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
E-mail: dnabank.brc@riken.jp
FAX: (+81)-29-836-9120

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(2011.07.25 T.M.)

2019.08.12