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Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes.

Steward CA, Humphray S, Plumb B, Jones MC, Quail MA, Rice S, Cox T, Davies R, Bonfield J, Keane TM, Nefedov M, de Jong PJ, Lyons P, Wicker L, Todd J, Hayashizaki Y, Gulban O, Danska J, Harrow J, Hubbard T, Rogers J, Adams DJ - Genomics (2009)

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.

View Article: PubMed Central - PubMed

Affiliation: The Wellcome Trust Sanger Institute, Hinxton, UK. cas@sanger.ac.uk

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Related in: MedlinePlus

NOD BAC clones are displayed on the Ensembl genome browser under the DAS sources, http://www.ebi.ac.uk/das-srv/genomicdas/das/nod_clones_m37 and http://www.ebi.ac.uk/das-srv/genomicdas/das/chori29_clones_m37. The NOD/MrkTac mouse strain is designated DIL NOD (Sanger/Ensembl prefix bQ) and the NOD/ShiLtJ mouse strain is designated CHORI-29 (Sanger/Ensembl prefix bCN). The DIL NOD clones are displayed as black and red bars and the CHORI-29 clones are displayed as blue and green bars, the colours indicating the orientation of the DNA insert in the vector. BAC clones on the forward strand are drawn above the DNA contig while clones on the reverse strand are drawn below. The clone end-reads are shown as small arrows in the corresponding color to the relevant BAC clone. Links to the end-read sequences in the Ensembl trace archive can be found by clicking on the clone end of interest.
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fig2: NOD BAC clones are displayed on the Ensembl genome browser under the DAS sources, http://www.ebi.ac.uk/das-srv/genomicdas/das/nod_clones_m37 and http://www.ebi.ac.uk/das-srv/genomicdas/das/chori29_clones_m37. The NOD/MrkTac mouse strain is designated DIL NOD (Sanger/Ensembl prefix bQ) and the NOD/ShiLtJ mouse strain is designated CHORI-29 (Sanger/Ensembl prefix bCN). The DIL NOD clones are displayed as black and red bars and the CHORI-29 clones are displayed as blue and green bars, the colours indicating the orientation of the DNA insert in the vector. BAC clones on the forward strand are drawn above the DNA contig while clones on the reverse strand are drawn below. The clone end-reads are shown as small arrows in the corresponding color to the relevant BAC clone. Links to the end-read sequences in the Ensembl trace archive can be found by clicking on the clone end of interest.

Mentions: To make the data accessible to the wider community, we have generated a Distributed Annotation System (DAS) [16] 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).


Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes.

Steward CA, Humphray S, Plumb B, Jones MC, Quail MA, Rice S, Cox T, Davies R, Bonfield J, Keane TM, Nefedov M, de Jong PJ, Lyons P, Wicker L, Todd J, Hayashizaki Y, Gulban O, Danska J, Harrow J, Hubbard T, Rogers J, Adams DJ - Genomics (2009)

NOD BAC clones are displayed on the Ensembl genome browser under the DAS sources, http://www.ebi.ac.uk/das-srv/genomicdas/das/nod_clones_m37 and http://www.ebi.ac.uk/das-srv/genomicdas/das/chori29_clones_m37. The NOD/MrkTac mouse strain is designated DIL NOD (Sanger/Ensembl prefix bQ) and the NOD/ShiLtJ mouse strain is designated CHORI-29 (Sanger/Ensembl prefix bCN). The DIL NOD clones are displayed as black and red bars and the CHORI-29 clones are displayed as blue and green bars, the colours indicating the orientation of the DNA insert in the vector. BAC clones on the forward strand are drawn above the DNA contig while clones on the reverse strand are drawn below. The clone end-reads are shown as small arrows in the corresponding color to the relevant BAC clone. Links to the end-read sequences in the Ensembl trace archive can be found by clicking on the clone end of interest.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2824108&req=5

fig2: NOD BAC clones are displayed on the Ensembl genome browser under the DAS sources, http://www.ebi.ac.uk/das-srv/genomicdas/das/nod_clones_m37 and http://www.ebi.ac.uk/das-srv/genomicdas/das/chori29_clones_m37. The NOD/MrkTac mouse strain is designated DIL NOD (Sanger/Ensembl prefix bQ) and the NOD/ShiLtJ mouse strain is designated CHORI-29 (Sanger/Ensembl prefix bCN). The DIL NOD clones are displayed as black and red bars and the CHORI-29 clones are displayed as blue and green bars, the colours indicating the orientation of the DNA insert in the vector. BAC clones on the forward strand are drawn above the DNA contig while clones on the reverse strand are drawn below. The clone end-reads are shown as small arrows in the corresponding color to the relevant BAC clone. Links to the end-read sequences in the Ensembl trace archive can be found by clicking on the clone end of interest.
Mentions: To make the data accessible to the wider community, we have generated a Distributed Annotation System (DAS) [16] 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).

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.

View Article: PubMed Central - PubMed

Affiliation: The Wellcome Trust Sanger Institute, Hinxton, UK. cas@sanger.ac.uk

Show MeSH
Related in: MedlinePlus