Journal
GENOMICS
Volume 95, Issue 2, Pages 105-110Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ygeno.2009.10.004
Keywords
Bacterial artificial chromosome; NOD/MrkTac; NOD/ShiLtJ; Mouse genome; Non-obese diabetic (NOD); Type 1 diabetes; T1D; Insulin-dependent diabetes; IDD
Funding
- National Institute of Allergy and Infectious Diseases, the National Institute of Diabetes, Digestive, and Kidney Disorders (both part of the National Institutes of Health)
- Juvenile Diabetes Research Foundation
- Medical Research Council, UK
- Wellcome Trust Sanger Institute
- Cancer Research, UK
- Medical Research Council [G0800024] Funding Source: researchfish
- National Institute for Health Research [NF-SI-0508-10275] Funding Source: researchfish
- MRC [G0800024] Funding Source: UKRI
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Non-obese diabetic (NOD) mice spontaneously develop type I 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. (C) 2009 Elsevier Inc. All rights reserved.
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