ORFeome Collaboration (OC)

– Our database is accessible HERE.

Highlights

– Untagged human ORFs, without native UTRs, without STOP codon, in promoterless Gateway Entry plasmids (Invitrogen).

– Approximately 10’800 ORFs, representing ca. 9’000 unique protein-coding genes.

– These ORFs can be easily shuttled towards expression plasmid through Gateway technologies.

– Created, from 2005 to 2011, by the “ORFeome Collaboration” (OC), a global consortium of numerous academic and commercial teams. The parental cDNAs were mostly derived from the Mammalian Gene Collection (MGC).

In more details

– These ORFs constructs contain neither a promoter nor a polyA sequence. For expression, they can be shuttled into Gateway Destination vectors (Invitrogen) by Gateway techniques. The restriction site-independence and high-fidelity of this method allows to perform this procedure on a large scale. Alternatively, standard subcloning methods can be used, provided that a STOP codon is included during the process (see below) and that the Kozak sequence is preserved.

– While the full ORFeome collection also comprises ORFs with STOP codon, we only acquired the subset of clones devoid of STOP codon. This allows maximal flexibility when shuttling the ORFs towards other Gateway Destination vectors, in particular for creating tagged or fusion constructs. Note that ORFs shuttled by Gateway techniques into a destination vector will contain a short tail of a few amino acids at their C-terminal end, corresponding to the Gateway recombination site.

– The clones have been fully sequence-verified during their construction. Importantly, this insures that their physical nucleotide sequence corresponds to their respective GenBank sequence, but this does not mean that they are free of “biological problems”. More details on this issue and on the way we can help HERE.

– This collection is not to be confused with the “human ORFeome” collection, whose current release is typically known as “hORFeome v8.1” and which was created by the CCSB in Boston. Despite being distinct, they collections overlap in 2 manners: both started in great part from the MGC cDNAs and therefore may contain similar isoforms and SNPs; a subset of the hORFeome collection was included in the ORFeome collaboration collection.

– When using an ORF from this collection in a publication, please refer to it as a “ORFeome Collaboration (OC) cDNA Clone”, and reference the web site http://www.orfeomecollaboration.org/ . The ID that should be indicated is the “IMAGE ID”, which is indicated in our Excel database.

MTA

– There is no restriction to the use of the clones and their derivatives for non-commercial applications. Nevertheless, transferring the clones outside of EPFL requires that the original MTA be included and that it is done free of charge. This requirement does not apply to derivatives of the clones (ORF subcloned in another vector for instance).

– If commercial applications are foreseen, please contact us for more details, in particular regarding the Gateway elements.

– The MTA can be found HERE.

Maps

– We provide the map upon distribution of the clones or upon request.

– The sequence of your ORF of interest, as well as a short stretch of flanking sequence, can be retrieved from GenBank by searching for the IMAGE ID of the clone (which is indicated in the Excel database). Be sure to type the term “image” in the GenBank search field in addition to the IMAGE ID number.

– Due to the decentralized nature of the OC consortium, different groups have contributed clones using their own preferred vectors and cloning strategies. For that reason, we cannot currently provide universal guidelines for assembling the maps on your own, but this is on our to do list.