The Orfeome Collaboration

Tools

The ORFeome Collaboration has the following tools available for public use:

Order ORF clones

Clone status search - find out if there is an ORF clone for your favorite gene
Get library/vector information
Plate availability query
ORFeome Query (OQ) - SQL-type query provides information about ORF clones and libraries
Download data via FTP

Other ORFeome Tools:
The following tools are from external sources; the data available may extend and/or overlap with that available from internal sources.

MGC/ORFeome Genome Browser (UCSC)
Search the DFCI-CCSB horfeome database (DFCI-CCSB)
Search the FLEXGene database (HIP)
Search the IMAGE IQ, which provides access to IMAGE clone data.

OC Collaborator Vector and Library Information

Center	Vector	3' End of attL1.x + seq to ATG	3' End of ORF to attL2.x
MGC	pENTR223.1 (SpnR)	-G TAC AAA AAA GCA GAA GGG CCG TCA AGG CCC ACC ATG- Y K K A E G P S R P T	-NNN GGC CTC ATG GGC CCA GCT TTC TTG TAC- G L M G P A F L Y
MGC (GENEART)	pENTR223.1 (SpnR)	-G TAC AAA AAA GCA GAA GGG CCG TCA AGG CCC ACC ATG- Y K K A E G P S R P T	-TAA GGC CTC ATG GGC CCA GCT TTC TTG TAC- * G L M G P A F L Y
MGC (GENEART)	pENTR223.1 (SpnR)	-G TAC AAA AAA GCA GAA GGG CCG TCA AGG CCC ACC ATG- Y K K A E G P S R P T	-TCA GGC CTC ATG GGC CCA GCT TTC TTG TAC- S G L M G P A F L Y
WTSI CMO	pENTR223 (SpnR)	-G TAC AAA AAA GTT GGC ACC ATG- Y K K V G T	-NNN CCA ACT TTC TTG TAC- P T F L Y
DF-CCSB CMO	pENTR223 (SpnR)	-G TAC AAA AAA GTT GGC ACC ATG- Y K K V G T	-NNN TTG CCA ACT TTC TTG TAC- L P T F L Y
DF-CCSB CMO	pENTR223 (SpnR)	-G TAC AAA AAA GTT GGC ATG- Y K K V G	-NNN TTG CCA ACT TTC TTG TAC- L P T F L Y
HIP	pENTR221 (KnR)	-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T	-TAG GAC CCA GCT TTC TTG TAC- * D P A F L Y ( closed/open with TAG suppr. )
HIP	pENTR221 (KnR)	-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T	-TTG GAC CCA GCT TTC TTG TAC- L D P A F L Y
DKFZ	pENTR221 (KnR)	-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T	-TGA ATC CAC CCA GCT TTC TTG TAC- * I P P A F L Y
DKFZ	pENTR221 (KnR)	-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T	-TGG ATC CAC CCA GCT TTC TTG TAC- W I H P A F L Y
DKFZ	pENTR221 (KnR)	-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T	-AAG CTT GAC CCA GCT TTC TTG TAC- K L D P A F L Y
DKFZ	pENTR221 (KnR)	-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T	-TGT ATT CAC CCA GCT TTC TTG TAC- C I H P A F L Y
DKFZ	pENTR221 (KnR)	-G TAC AAA AAA GCT GGC ACC ATG- Y K K A G T	-GGC GAC CCA GCT TTC TTG TAC- G D P A F L Y
DKFZ	pENTR221 (KnR)	-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T	-TAG CTT GAC CCA GCT TTC TTG TAC- * L D P A F L Y
DKFZ	pENTR221 (KnR)	-G TAC AAA AAA GCA GGC TCC ACC ATG- Y K K A G S T	-TGA ATT CAC CCA GCT TTC TTG TAC- * I P P A F L Y
DKFZ	pENTR201 (KnR)	-G TAC AAA AAA GCT GGC ACC ATG- Y K K A G T	-GGC GAC CCA GCT TTC TTG TAC- G D P A F L Y
DKFZ	pENTR201 (KnR)	-G TAC AAA AAA GCT GGC ACC ACC ATG- Y K K A G T	-TAG GGC GAC CCA GCT TTC TTG TAC- * G D P A F L Y
DKFZ	pENTR/D-TOPO (KnR)	-G TAC AAA AAA GCA GGC TCC GCG GCC GCC CCC TTC ACC ATG- Y K K A G S A A A P F T	-AGG GGT GGG CGC GCC GAC CCA GCT TTC TTG TAC- K G G R A D P A F L Y
Kazusa	pENTR201 (KnR)	-G TAC AAA AAA GCA GGC TTC GAA GGA GAT AGA ACC ATG- Y K K A G F E G D R T	-TAA GTA GAC CCA GCT TTC TTG TAC- * V D P A F L Y -TAC GTA GAC CCA GCT TTC TTG TAC- Y V D P A F L Y
Invitrogen	pENTR221 (KnR)	-G TAC AAA AAA GCA GGC ACC ATG- Y K K A G T	-TAG AAC CCA GCT TTC TTG TAC- * T P A F L Y
Invitrogen	pENTR201 (KnR)	-G TAC AAA AAA GCA GGC TTC GAA GGA GAT AGA ACC ATG- Y K K A G F E G D R T	-TAG GAC CCA GCT TTC TTG TAC- * D P A F L Y ( closed/open with TAG suppr. )

Cloning Method Overview (CMO)

Wellcome Trust Sanger Institute

ORFs flanked by att sites were amplified from fully sequence verified cDNA clones in two rounds of PCR. Amplified products were separated by agarose gel electrophoresis, excised, purified and recombined into pDONR223 using BP® clonase. After full sequence verification, only clones which exactly matched the original cDNA and att sequences were accepted.

Dana Farber Cancer Institute

MGC clones were cherry-picked into a non-redundant set and 8 ul of each clone was inoculated in 1 ml LB containing either ampicillin (100 ug/ml) or chloramphenicol (34 ug/ml) depending on the MGC vector. A BP recombinational reaction contains 2 ul of 5 X BP3 buffer; 2 ul of BP clonase; 1 ul of pDONR223 (150 ng/uL); 2 ul of PCR product (2-200 ng/uL); 3 uL H2O. The 5 X BP3 buffer consists of 100 mM Tris-Cl (pH 7.5); 20 mM EDTA; 30 mM spermidine-HCL; 25% glycerol; 225 mM NaCl. LR reactions we performed as described previously with minor changes (Reboul et al. 2003, Rual et al. 2004). BP products were transformed into liquid cultures of E. coli, with antibiotic selection of spectinomycin at 50 ug/mL.