title: Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes.
abstract: 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.
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, UK. cas@sanger.ac.uk
authors.forename: Charles A
authors.initials: CA
authors.lastname: Steward
authors.forename: Sean
authors.initials: S
authors.lastname: Humphray
authors.forename: Bob
authors.initials: B
authors.lastname: Plumb
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Jones
authors.forename: Michael A
authors.initials: MA
authors.lastname: Quail
authors.forename: Stephen
authors.initials: S
authors.lastname: Rice
authors.forename: Tony
authors.initials: T
authors.lastname: Cox
authors.forename: Rob
authors.initials: R
authors.lastname: Davies
authors.forename: James
authors.initials: J
authors.lastname: Bonfield
authors.forename: Thomas M
authors.initials: TM
authors.lastname: Keane
authors.forename: Michael
authors.initials: M
authors.lastname: Nefedov
authors.forename: Pieter J
authors.initials: PJ
authors.lastname: de Jong
authors.forename: Paul
authors.initials: P
authors.lastname: Lyons
authors.forename: Linda
authors.initials: L
authors.lastname: Wicker
authors.forename: John
authors.initials: J
authors.lastname: Todd
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
authors.forename: Omid
authors.initials: O
authors.lastname: Gulban
authors.forename: Jayne
authors.initials: J
authors.lastname: Danska
authors.forename: Jen
authors.initials: J
authors.lastname: Harrow
authors.forename: Tim
authors.initials: T
authors.lastname: Hubbard
authors.forename: Jane
authors.initials: J
authors.lastname: Rogers
authors.forename: David J
authors.initials: DJ
authors.lastname: Adams
mesh_terms: 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
chemical_list: D018076:DNA, Complementary