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CHORI-252: Vervet Monkey BAC Library |
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The CHORI-252 vervet monkey BAC library has been constructed by Michael Nefedov in Pieter de Jong’s laboratory at BACPAC Resources, Children’s Hospital Oakland Research Institute. The preparation of the library followed the cloning approach developed in our laboratory (Osoegawa et al., 1998). A blood sample was obtained from an adult male vervet monkey (#1994-021) through Roel A. Ophoff (Center for Neurobehavioral Genetics, UCLA) and Lynn A. Fairbanks (Center for Primate Neuroethology, UCLA). DNA was isolated from white blood cells by embedding the cells in agarose. Agarose embedded high molecular weight DNA was partially digested with a combination of EcoRI restriction enzyme and EcoRI Methylase. The DNA fragments were size-fractionated by pulsed field electrophoresis and DNA fragments from the appropriate size fraction were cloned into the pTARBAC2.1 vector between the EcoRI sites. The ligation products were then transformed into DH10B (T1 resistant) electrocompetent cells (Invitrogen). The library has been arrayed into 384-well microtiter dishes and also gridded onto eleven 22x22cm nylon high-density filters for screening by probe hybridization. Each hybridization membrane represents over 18,000 distinct vervet monkey BAC clones, stamped in duplicate. Library characterization was performed by Qing Cao and Kazutoyo Osoegawa. This work was funded by NIH grant HG01165-06.
Note: This BAC library has been used for large-scale physical mapping by BAC-end sequencing and comparative alignment of the BAC-end Sequences (BES) relative to the human and rhesis macaque genome assemblies. One can search for BACs containing any "putative" vervet genes by looking for those genes in the UCSC Human Genome Browser displaying a custom track of the CHORI-252 BACs relative to the human genome. The BAC-end sequences were obtained at McGill University, Montreal as funded by Genome Quebec and Genome Canada. More information can be found at websites displaying the Vervet Monkey Physical Map Project and the Integrated Vervet Monkey Genomic Resources. From the Physical Map Project URL, one can upload all the mapped BAC-end Sequences to the UCSC Human Genome Browser by following the recommendation "You can go directly to the UCSC Genome Browser here " .
| Segment | Cloning Vector | DNA | Restriction enzyme | Plate Number | Total Plates | Empty Wells | Empty Wells (%) | | 1 | pTARBAC2.1 | Blood | EcoRI | 1-288 | 288 | 1,236 | 1.1 | | 2 | pTARBAC2.1 | Blood | EcoRI | 289-528 | 240 | 726 | 0.8 | | Total Library | | | | | 528 | 1,962 | 1 |
| Segment | Non-insert Clones (%) | Non-insert Clones (deleted vector) | Non-recombinant Clones (vector) | Recombinant Clones | Insert Size (Average) | Redundancy (Genome Size: 3,000 Mb) | | 1 | 0.4 | ~ 400 | 13 | 110,000 | 160 Kbp | 5.9 | | 2 | 0 | ~ 0 | 15 | 91,000 | 160 Kbp | 4.9 | | Total library | 0.2 | ~ 400 | 28 | .201,000 | 160 Kbp | 10.8 |
click here for a legend of the previous tables.
Data on the CHORI-252 clone average insert size has been determined by Pulsed Field Gel Electrophoresis. Clone size distribution has been plotted graphically.
Individual clones identified after screening can be obtained as stab cultures at a cost of $80 per clone in addition to a $35 set-up charge per shipment. Shipping will be done by Federal Express and charged to recipient's account number.
With respect to the scheduling of shipments of arrayed library copies, we would like to make you aware of our policy for array distribution.
Please visit the ordering information page if you want to place an order.
Academic and commercial users interested in a copy of the BAC library should contact Pieter J. de Jong ([email protected], fax: (510) 450-7924). For hybridization membranes, please contact BACPAC Resources ([email protected]).
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