1. Introduction

Genomic and transcriptome research have provided for more than a decade a fast amount of sequence information. Initiated by the Human Genome Sequencing Project, by now a large number of entire genomes has been sequenced; a trend that will grow even faster with the availability of new high-speed sequencing methods. Along with sequencing projects efforts have been made to establish also comprehensive genomic DNA and cDNA collections from model organisms like for instance human, mouse, Drosophila, and C. elegans, or plants like Arabidopsis and rice. From the original cDNA collections, cloning projects have moved on to transferring coding regions of cDNAs to entry and expression vectors for functional studies on a genome-wide scale. Moreover, recent developments in the discovery of new classes of non-coding RNAs have let to entirely new resources comprising RNAi and miRNA expression clones. All these efforts from those large-scale projects let to the establishment of huge clone collections that have to be shared among the research community to exploit their true value. Hence, competent solutions and services are now needed to utilize these valuable resources and to provide each researcher with the clone(s) he or she wants. Whereas in the past the exchange of research materials happened between individual researchers, the huge resources from large-scale projects require now other means for sharing the materials depending on dedicated resource centers and providers. These resource centers have to take on the responsibility to maintain the clone collections, and to provide individual clones or copies of entire clone collections to the end users. As a collaborator of large-scale international research project and generator of large cDNA collections using our own full-length cDNA cloning method, DNAFORM is committed to providing the research community both at academic and commercial research organizations with first class clone distribution services.

2. What Can Public Clone Collections Offer to the Research Community?

The concept of modern science is based on the principle of sharing information and to make published materials available to others. By having access to clones in the public domain you can:

• Find the clones that match with sequence information in public databases.
• Obtain characterized clones for your work.
• Easy and fast access to the clones of your interest.
• Timely delivery by professional providers.

If you obtained partial sequence information for an interesting player in your system, find the matching cDNA in a public database and get the right clone of clones to perform your stusdies. Wherever you require additional controls to do your experiments, or you would like to open up new aspects to your research, public resources can offer the clones you need. Sharing common resources is our gateway to the future of life science. DNAFORM wants to be your partner to fulfill this mission.

3. Limitation of Public Clone Collections

Public clone collections by now comprise literally millions of clones. Althouch generally prepared with great care, collections comprising millions of clones cannot be free of errors! Common errors in clone collections are:

• ID error: Stored clone and related information do not match.
• Annotation error: Clone related information is not correct.
• Sequencing error: Clone related sequence information contains mistakes.
• Dead clones/missing clones: Clone is no longer available.
• Contamination: Clone stock got contaminated by other clone or microorganism.
• Outdated information: Annotation information for many clones is not updated by the originator. Therefore project specific databases may be outdated.

Depending on the originator of the resources efforts are made to correct mistakes in the clone collections and related databases. In additions, clone distributors keep records on clone and annotation errors to take wrong clones out of their distribution lists. However, no matter how much efforts are being made, there will never be entirely error-free clone collections, since even well QC-controlled clone collections can loose clones over time. In addition, clones with ID errors are in many cases hard to be replaced, if the mistake occurred already on the original master plates given out to the resource centers and distributors. Therefore all users of public clone collections are advised to check their clones prior to use in their experiments. The easiest way to avoid any risk of obtaining and using wrong clones is to order clones on which the distributor has performed an ID check already before shipping out the materials. Most commonly, distributors confirm the ID of a clone by obtaining partial sequence information and aligning it to the clone sequence in the database. The ID check will make sure that you get the clone you want; though it cannot exclude mistakes in clone related annotations and sequencing errors in database entries. Note, ID checks are usually only performed for individual clones. Re-sequencing entire plate or even clone collections is very costly, and will only be done on request.

4. How to find your Clone of Interest?

Seeing the large number of clones out in the public domain, specific clones can only be identified by searching different databases. Many large cloning project like the RIKEN FANTOM and NIH MGC/IMAGE projects have their own clone tracking and annotation databases. In addition, for most clones the sequences have been submitted to NCBI, EMBLE, and DDBJ, and can be found in those key public databases. In addition, distributors often have their own clone database to provide clone related information. To support our customers and to make searching, selection, and ordering of clones as convenient as possible, DNAFORM has established the DNAFORM Clone Search Engine. The DNAFORM Clone Search Engine provides full support in English and Japanese and enables our customers to search for clones and/or clone related information by:

• Search by clone or gene ID: Use any clone or gene ID to find matching clones in our cDNA collections.
• Search by plate address: This function addresses the needs of customers who purchased plates comprising multiple clones. By using clone or plate specific coordinates, clone related information can be retrieved from the database.
• Search by BLAST nucleotide sequence: This function allows you to find clones in our database that share in part or over the entire length sequence homology to clones in our collections.

For all clones in the DNAFORM Clone Search Engine we provide links to the latest annotation information at NCBI.

Presently the DNAFORM Clone Search Engine provides information on cDNA clones from the RIKEN FANTOM, RIKEN human cDNAs, RIKEN human ORF entry clones, RIKEN honeybee clone collections, NIH MGC, NIH ORFeome, and NKI shRNA projects. DNAFORM is working constantly on expanding the content of the DNAFORM Clone Search Engine by adding more clone related information and new resources.

5. Overview on Genomic Resources from DNAFORM and Geneservice

DNAFORM and Geneservice, a leading UK-based provider of genomic resources, have entered into a partnership to provide the research community with one of the world's most comprehensive product range on genomic resources presently comprising more than 16 million DNA samples. We are actively working together with the research community to continuously make new resources available, and to expand our portfolio by adding innovative resources like for example new ORF clones, RNAi expression clones such as the human shRNAs, or proteomic resources as the phage display libraries. Highlight from our present program include:

• RIKEN FANTOM Clone Collection - The world's biggest cDNA collection obtained from a single organism.
• cDNA Resources - Besides the RIKEN FANTOM Clone Collection, large cDNA resources are available out of the MGC collection and IMAGE Resources. There resources include cDNA clones from Human, Mouse, Rat, Cow, Chicken, Drosophila, Xenopus, Zebrafish, C. elegans, and C. jejuni as well as RIKEN honeybee cDNA clone collection.
• DNA Aliquots - Whole Genome Amplified DNA samples are available for genomic DNA from Human, Mouse, Rat, Dog, Cow, Chicken, S. cerevisiae, and Fugu.
• Genomic DNA Clones - Genomic DNA clones are available from Human, Mouse, Dog, Pig, Chicken, Drosophila, Fugu, and C. elegans.
• ORF Clones - Entire ORF collections are offered from C. elegans, and C. jejuni. We have also started the distribution of human ORF clones from NIH ORFeome Project.
• Proteomic Resources - Phage display libraries to screen for specific antibodies for your molecules of interest. The artificial Human Single Fold scFv antibody library can be used to derive binders to almost any target molecule using phage display and target selection.
• miRNA/RNAi - A Human miRNA set and RNAi resources for C. elegans are available including the new human shRNA resource from the NKI.
• Sanger - Resources from the renown Sanger Center include predicted ORF's for human chromosome 22 and mouse genomic clones.