Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes.
Non-obese diabetic (NOD) mice spontaneously develop type 1 diabetes (T1D) due to the progressive loss of insulin-secreting beta-cells by an autoimmune driven process. NOD mice represent a valuable tool for studying the genetics of T1D and for evaluating therapeutic interventions. Here we describe the development and characterization by end-sequencing of bacterial artificial chromosome (BAC) libraries derived from NOD/MrkTac (DIL NOD) and NOD/ShiLtJ (CHORI-29), two commonly used NOD substrains. The DIL NOD library is composed of 196,032 BACs and the CHORI-29 library is composed of 110,976 BACs. The average depth of genome coverage of the DIL NOD library, estimated from mapping the BAC end-sequences to the reference mouse genome sequence, was 7.1-fold across the autosomes and 6.6-fold across the X chromosome. Clones from this library have an average insert size of 150 kb and map to over 95.6% of the reference mouse genome assembly (NCBIm37), covering 98.8% of Ensembl mouse genes. 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. Clones from this library have an average insert size of 205 kb and map to 93.9% of the reference mouse genome assembly, covering 95.7% of Ensembl genes. We have identified and validated 191,841 single nucleotide polymorphisms (SNPs) for DIL NOD and 114,380 SNPs for CHORI-29. 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.
Steward
Charles A
CA
The Wellcome Trust Sanger Institute, Hinxton, UK. cas@sanger.ac.uk
Humphray
Sean
S
Plumb
Bob
B
Jones
Matthew C
MC
Quail
Michael A
MA
Rice
Stephen
S
Cox
Tony
T
Davies
Rob
R
Bonfield
James
J
Keane
Thomas M
TM
Nefedov
Michael
M
de Jong
Pieter J
PJ
Lyons
Paul
P
Wicker
Linda
L
Todd
John
J
Hayashizaki
Yoshihide
Y
Gulban
Omid
O
Danska
Jayne
J
Harrow
Jen
J
Hubbard
Tim
T
Rogers
Jane
J
Adams
David J
DJ
D000818:Animals; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics* / Q000378:metabolism; D018076:DNA, Complementary / Q000378:metabolism; D016678:Genome; D008297:Male; D051379:Mice; D016688:Mice, Inbred NOD; D008815:Mice, Inbred Strains; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA
D018076:DNA, Complementary