Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes.
Bottom Line: By the same metric, the CHORI-29 library has an average depth over the autosomes of 5.0-fold and 2.8-fold coverage of the X chromosome, the reduced X chromosome coverage being due to the use of a male donor for this library.In total we generated 229,736,133 bp of sequence for the DIL NOD and 121,963,211 bp for the CHORI-29.These BAC libraries represent a powerful resource for functional studies, such as gene targeting in NOD embryonic stem (ES) cell lines, and for sequencing and mapping experiments.
Affiliation: The Wellcome Trust Sanger Institute, Hinxton, UK. email@example.comShow MeSH
Related in: MedlinePlus
Mentions: To make the data accessible to the wider community, we have generated a Distributed Annotation System (DAS)  source to display both the DIL NOD clones (http://www.ebi.ac.uk/das-srv/genomicdas/das/nod_clones_m37) and the CHORI-29 clones (http://www.ebi.ac.uk/das-srv/genomicdas/das/chori29_clones_m37) so that they can be visualized in DAS source compliant browsers. For example, in the Ensembl genome browser (http://www.ensembl.org/Mus_musculus/Info/Index) the alignments of both NOD BAC libraries can be accessed through the DAS sources menu and viewed against the reference C57BL/6J genome. DIL NOD clones are displayed as red and black lines depending on the orientation of the insert in the vector, while CHORI-29 clones are displayed as green and blue lines. The BAC end-sequences can also be viewed as traces in the main “Region in Detail” window of the Ensembl genome browser. The method used to display BAC ends in Ensembl shows only those that have corresponding ends that are considered to be within 3 standard deviations of the mean insert size of the library. End-reads provide a link to the Ensembl trace repository (http://trace.ensembl.org), where the end-read sequences for all quality clipped reads have been deposited (Fig. 2). FASTA files of these quality clipped reads have also been generated and deposited on the Sanger FTP site (ftp://ftp.sanger.ac.uk/pub/NODmouse/NOD_BACend_fasta_sequences).
Affiliation: The Wellcome Trust Sanger Institute, Hinxton, UK. firstname.lastname@example.org