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CHORI-212: Channel Catfish (Icalurus punctatus) BAC Library |
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The CHORI-212 Channel Catfish (Icalurus punctatus) BAC library has been constructed by Jim Thorsen and Dr. Baoli Zhu in Pieter de Jong's laboratory at BACPAC Resources, Children's Hospital Oakland Research Institute. The library preparation followed the general cloning approach developed in our laboratory (Osoegawa et al., 1998). High-molecular-weight DNA was prepared from nucleated blood cells derived from a male channel catfish (USDA103 strain) by Dr. Geoffrey C. Waldbieser (USDA-Agricultural Research Service). Approximately 3.6 x 107 cells were embedded in ~ 50 agarose blocks, thus each block contains ~7.5 x 105 cells. Agarose-embedded DNA was partially-digested with a mixture of EcoRI restriction enzyme and EcoRI Methylase. The digested DNA was subsequently size-fractionated using pulsed-field gel electrophoresis. DNA of the desired size fraction was ligated into the pTARBAC2.1 vector between the EcoRI sites. The ligation products were transformed into DH10B (T1-resistant) electro-competent cells (Invitrogen). The BAC library has been arrayed into 384-well microtiter dishes. The arrayed clone collection can be screened by probe hybridization using 22x22cm nylon high-density filters. Each hybridization membrane represents about 18,000 distinct BAC clones (from 48 distinct 384-well microtiter dishes) stamped in duplicate on.
BAC library construction was funded by a grant from USDA (99-35205-8537).
Provisional data for CHORI-212 Channel Catfish BAC Library:
Segment | 1 | All | Vector | pTARBAC2.1 | pTARBAC2.1 | Restriction Enzyme | EcoRI/EcoRI Methylase | EcoRI/EcoRI Methylase | DNA Source | blood | blood | Plate Numbers | 1-192 | 1-192 | Plate Count | 192 | 192 | Empty Wells | 1174 (1.59%) | 1174 (1.59%) | Non-Recombinant Clones | 52 (0.07%) | 52 (0.07%) | Non-Insert Clones | Approx. 435 (0.6%) | Approx. 435 (0.6%) | Recombinant Clones | 72067 | 72067 | Average Insert Size | 161 Kbp | 161 Kbp | Genomic Coverage | 10.6X | 10.6X |
Click here for legend of the previous table.
No clones were found to be non-recombinant after analysis of CHORI-212 using overgo probes specific for the puc19 fragment.
Data on the CHORI-212 clone insert size distribution has been determined by pulsed-field gel Electrophoresis. Clone Size Distribution has been plotted graphically.
Further in depth characterization of the library is on going in our lab and data will be updated on our web page periodically.
Please direct questions concerning this library to either Pieter J. de Jong or Kazutoyo Osoegawa .
Ordering & Pricing information
The library is available in several formats. Individual clones, and high-density hybridization filter are obtainable. For ordering and shipping details, please view the ordering and pricing information ordering and pricing information page.
Academic and commercial users interested in a copy of the BAC library should contact Pieter J. de Jong (pdejong@chori.org, fax: (510) 450-7924).
Reference
Dr. Geoffrey C. Waldbieser
e-mail:gwaldbieser@ars.usda.gov
USDA-Agricultural Research Service
Catfish Genetics Research Unit
141 Experiment Station Road
Stoneville, Mississippi, 38776
USA
The genome size (1.1 Gb) of the catfish has been described in the following references:
Tiersch, T. R., and C. A. Goudie (1993) Inheritance and variation of genome size in half-sib families of hybrid ictalurid catfishes. J. Hered. 84: 122-125.
Tiersch, T. R., B. A. Simco, K. B. Davis, R. W. Chandler, S. S. Wachtel et al., (1990) Stability of genome size among stocks of channel catfish. Aquaculture 87: 15-22.
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