Michael,
As you may know, the RP11 library was made in my lab when it was located at the Roswell Park Cancer Institute. The NIH grant & library distribution & library makers moved in 1999 to a new location: CHORI, Oakland. With respect to your question: clones are named according to the NCBI Nomenclature rules and the number "8915" represent the number of the microtiter dish containing the specific clone which was BAC-end sequenced. You are correct to state that the largest dish number in the library is "1440". How to explain the number "8915"? The BAC-end sequence records for this clone describe the clone name and the sequencing center where the data was generated: High Throughput Sequencing Center, University of Washington, Seattle. All of the BAC-end sequencing work was done in the late nineties and I was surprised to find that the data record carries a more recent date: May 9, 2010. <http://www.ncbi.nlm.nih.gov/nucgss/6355724?report=genbank> http://www.ncbi.nlm.nih.gov/nucgss/6355724?report=genbank Anyhow, when the sequencing was done in Seattle for ~100,000 BACs, it preceded the Capillary Sanger Sequencing method and 96-well DNA prep methods. Hence, the library was re-arrayed from 384 to 96-well format and a different dish numbering system was used. DNA preparations were done in 8-tube racks, thus requiring a lot of reformatting and sequenced on ABI slab gels. Initially all BAC-ends generated used the provisional "intermediate" dish numbers in the BAC-end sequence records. These were long ago corrected to reflect the original 384 well dishes. I do not currently have access to the translation and will try to find this and then correct the data. The short answer: it's a correct clone but with an intermediat dish ID attached. Pieter J. de Jong, Ph.D. Principal Investigator KOMP-CSD & Director, BACPAC Resources Center Children's Hospital Oakland Research Institute Phone: 510-450-7919 (direct); -450-7927 (admin.coordinator) Fax: 510-450-7951; [email protected] Website: http://bacpac.chori.org -----Original Message----- From: [email protected] [ <mailto:[email protected]> mailto:[email protected]] On Behalf Of Bianchi, Michael Sent: Wednesday, August 25, 2010 5:34 AM To: '[email protected]' Subject: [Genome] BAC Clone question I have a question regargding the validity of a clone that is present in the database. The clone is RP11-8915J21. There are only 5 segments of this library and the largest number that is present in the 5th segment of the library is 1440. Would it be possible to find out where the information about this clone came from? Thanks for your help, Mike Michael Bianchi BLSC, Rm. L1-125 Genomics Shared Resource Department of Cancer Genetics Roswell Park Cancer Institute Elm & Carlton Streets Buffalo, NY 14263 Phone: 716-845-3531 Email: [email protected]< <mailto:[email protected]> mailto:[email protected]> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
