Finding cDNA clones

From OpenWetWare

Jump to: navigation, search

Several partly overlapping initiatives have been generating and providing cDNA clones, i.e. reverse transcribed copies of mRNAs. Due to the academic or academic+commercial backbone of these enterprises, clones are available for relatively low costs, typically around 70€/50£/?$. As of 2008, clones are provided in Europe by GeneService and imaGenes (prev RZPD), and in N America by the ATCC/LGC Promochem.

Finding and checking candidate clones

There is a confusing number of cDNA clones and an even larger number of EST clones linked to most genes, esp. from humans and mouse. The tools below help you to select:

  • Many gene entries in the NCBI database are linked to cDNA clones. Look out for order cDNA clones (top right). Example: TUBB [1] (human β-tubulin) and its NCBI-linked cDNA clones [2].
  • Check the MGC (Mammalian Gene Collection), a collection of full-length cDNA clones for human, mouse, rat, and cow genes. The MGC selects cDNA clones from various libraries if they satisfy their criteria for full-length clones.
  • Blast your mRNA of interest against a set of cDNA clones using for example the RZPD/imaGenes tool. The tool align known sequences from the clones with the mRNA search query which gives you an idea of whether you are looking at a full cDNA clone.
  • If you cannot find anything, have a look at the UniGene entry for your gene. It contains an expandable list of EST clones (generally fragments for the full cDNA). Look out for the label PM, which stands for could be translated into Protein and is full length according to MGC.
  • query the IMAGE database, a now superseded consortium for the generation and distribution of cDNA clones; get the sequencing information for a clone of interest and align it to your mRNA of interested using tools like blast2seq

Purchase clones

cDNA clones are available through several distributors with overlapping regional limits. European distributors like GeneService and imaGenes stock most of the old IMAGE libraries. The remaining material is being transferred to a "company associated with Open Biosystems". This can cause big differences in ordering time, since if the clone you want is not in company stocks it has to be ordered from this company.

Watch out for prices. Different distributors may charge different prices for the same clone. This could be explained by different quality checks done by the companies or just by customers not comparing costs. For example, the typical IMAGE cDNA clone without additional sequencing by the company costs £52 (70€ [3]) from GeneService, UK while it costs 89€ from imaGenes, D.

Companies offer additional verification by sequencing. However, many clones have been checked after generation. Sequences can be obtained via the IMAGE website.

Links

distributors

  • geneservice based in UK, distributes to Europe
  • ImaGenes based in Germany, distributes to Europe
  • ATCC/LGC based in USA, distributes to N America
  • some clones are also available via Invitrogen and Open Biosystems
Personal tools