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CHORI-211: Zebrafish Tue (Tuebingen) strain (Danio rerio) BAC Library |
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The CHORI-211 Tue strain Zebrafish Danio rerio BAC library has been constructed by Chung Li Shu and Dr. Kazutoyo Osoegawa in Pieter De Jong's Laboratory at BACPAC Resources, Children’s Hospital Oakland Research Institute. Genomic DNA was isolated from testis of 6 males by Dr. Gerd-Joerg Rauch and partially digested with a combination of EcoRI and EcoRI Methylase. Size selected DNA was cloned into the pTARBAC2.1 vector between the EcoRI sites. The ligation products were transformed into DH10B electro-competent cells (BRL LIFE TECHNOLOGIES). The library has been arrayed into 384-well microtiter dishes and also gridded onto six 22x22cm nylon high-density filters for screening by probe hybridization. Each hybridization membrane represents over 18,000 distinct zebrafish BAC clones, stamped in duplicate. Library construction was supported by sub-contracts from a grant awarded to Dr. Robert Geisler at The Max-Planck-Institut fuer Entwicklungsbiologie. The clones from his BAC library have been used as part of the clone-based sequencing project at the Sanger Institute in the UK and the clone-fingerprinting projects at the Max Planx Institute in Germany. The clones can be found in various public databases using either the "internal" Sanger nomenclature or the "external" NCBI recommended nomenclature. For example, CH211-15B7 (NCBI nomenclature) corresponds to the clone found in microtiter dish (384-well type) #15, at the intersection of row "15 and column "7". The same clone in the "internal" Sanger nomenclature is labeled as: "zC15B7". When ordering clones from BACPAC Resources Center (BPRC, @CHORI) using the online ordering system, please use the NCBI nomenclature.
Overviews of the BAC and fosmid libraries used for the zebrafish sequencing and mapping projects can be found at the Sanger "Fingerprinting web page" and the Sanger "Zebrafish Libraries" page.
Provisional data for CHORI-211 Zebrafish Tue strain Dani rerio BAC Library:
Segment | 1 | 2 | All | Vector | pTARBAC2.1 | pTARBAC2.1 | pTARBAC2.1 | Restriction Enzyme | EcoRI/EcoRI Methylase | EcoRI/EcoRI Methylase | EcoRI/EcoRI Methylase | DNA Source | sperm | sperm | sperm | Plate Numbers | 1-144 | 145-288 | 1-288 | Plate Count | 144 | 144 | 288 | Empty Wells | 1314 (2.38%) | 1278 (2.31%) | 2592 (2.34%) | Non-Recombinant Clones | 0 (0%) | 41 (0.08%) | 41 (0.04%) | Non-Insert Clones | Approx. 648 (1.2%) | Approx. 1404 (2.6%) | Approx. 4104 (3.8%) | Recombinant Clones | 53334 | 52573 | 103855 | Average Insert Size | 171 Kbp | 160 Kbp | 165.7 Kbp | Genomic Coverage | 5.4X | 5X | 10.4X |
Click here for legend of the previous table.
No clones were found to be non-recombinant after analysis of CHORI-211 using overgo probes specific for the puc19 fragment.
Data on the CHORI-211 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.
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 ([email protected], fax: (510) 450-7924).
Reference
The characteristics of Tue (Tuebingen) zebrafish line are described in the following paper:
Rauch, G.-J., Granato, M. and Haffter, P. (1997). A polymorphic zebrafish line for genetic mapping using SSLPs on high-percentage agarose gels. Technical Tips Online T01208.
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