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CHORI-29: NOD Mouse (Mus musculus) BAC Library |
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The CHORI-29 NOD/LtJ mouse Mus musculus BAC library has been constructed by Dr. 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. The mouse sample was obtained through the Jackson Laboratory. DNA was isolated from kidney cells of a Mus musculus NOD/LtJ mouse . Agarose-embedded high molecular weight DNA was partially digested with EcoRI/EcoRI Methylase restriction enzyme. Size fractionated DNA was ligated into the pTARBAC2.1 vector between the EcoRI sites. The ligation products were transformed into DH10B (T1 resistant) electrocompetent cells (Invitrogen). The library has been arrayed into 384-well microtiter dishes. The 22x22cm nylon high-density filters have been made available for probe hybridization screening.
Library characterization (see below) was performed by Qing Cao, Boudewijn ten Hallers and Kazutoyo Osoegawa.
Please note: Many clones (>100,000) of the library have been "BAC-end sequenced" at the Sanger Institute and this has resulted in 206,971 BAC-end sequences stored in the NCBI Trace_Archive. The end-sequences have permitted aligning the BAC clones to the sequenced mouse genome (from a different mouse strain, C57BL/6J). The aligned ("mapped") BAC clones can currently be found in two ways: 1)Displayed in the ENSEMBL (after configuring the browser display), or 2)By searching the NCBI CloneFinder (Cf) program. Please note that these databases follow different naming "dialects" for the BAC clones. The clones found through ENSEMBL have the following format: "bCN538a05". The same clone in CloneFinder is named: "CH29-538A5", which is the NCBI standard nomenclature used for more 10 years. BACPAC Resources has an online ordering system and this uses the NCBI Nomenclature. Therefore, clone names found on the ENSEMBL site should be translated into NCBI format to be recognized by the BACPAC electronic shopping cart. ["bCN" becomes "CH29-" and an extra digit in the "column" number should be removed: "05" should become "5"].
Provisional data for CHORI-29 NOD/LtJ mouse (Mus musculus) BAC Library:
Segment | 1 | 2 | 3 | 4 | All | Vector | pTARBAC2.1 | pTARBAC2.1 | pTARBAC2.1 | pTARBAC2.1 |
| Restriction Enzyme | EcoRI/EcoRI Methylase | EcoRI/EcoRI Methylase | EcoRI/EcoRI Methylase | EcoRI/EcoRI Methylase | N/A | DNA Source | kidney | kidney | kidney | kidney | N/A | Plate Numbers | 1-288 | 289-480 | 481-720 | 721-960 | 1-960 | Plate Count | 288 | 192 | 240 | 240 | 960 | Empty Wells | 2883 (2.61%) | 1757 (2.38%) | 2186 (2.37%) | 2152 (2.34%) | 8978 (2.44%) | Non-Recombinant Clones | N/A | N/A | N/A | N/A | N/A | Non-Insert Clones | N/A | N/A | N/A | N/A | N/A | Recombinant Clones | 107709 | 71971 | 89974 | 90008 | 359662 | Average Insert Size | N/A | N/A | 160 Kbp | 157 Kbp | N/A | Genomic Coverage | N/A | N/A | N/A | N/A | N/A |
Click here for legend of the previous table.
No clones were found to be non-recombinant after analysis of CHORI-29 using overgo probes specific for the puc19 fragment.
Data on the CHORI-29 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 click here.
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
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