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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 β-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 d...

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Autores principales: Steward, Charles A., Humphray, Sean, Plumb, Bob, Jones, Matthew C., Quail, Michael A., Rice, Stephen, Cox, Tony, Davies, Rob, Bonfield, James, Keane, Thomas M., Nefedov, Michael, de Jong, Pieter J., Lyons, Paul, Wicker, Linda, Todd, John, Hayashizaki, Yoshihide, Gulban, Omid, Danska, Jayne, Harrow, Jen, Hubbard, Tim, Rogers, Jane, Adams, David J.
Formato: Texto
Lenguaje:English
Publicado: Academic Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824108/
https://www.ncbi.nlm.nih.gov/pubmed/19909804
http://dx.doi.org/10.1016/j.ygeno.2009.10.004
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author Steward, Charles A.
Humphray, Sean
Plumb, Bob
Jones, Matthew C.
Quail, Michael A.
Rice, Stephen
Cox, Tony
Davies, Rob
Bonfield, James
Keane, Thomas M.
Nefedov, Michael
de Jong, Pieter J.
Lyons, Paul
Wicker, Linda
Todd, John
Hayashizaki, Yoshihide
Gulban, Omid
Danska, Jayne
Harrow, Jen
Hubbard, Tim
Rogers, Jane
Adams, David J.
author_facet Steward, Charles A.
Humphray, Sean
Plumb, Bob
Jones, Matthew C.
Quail, Michael A.
Rice, Stephen
Cox, Tony
Davies, Rob
Bonfield, James
Keane, Thomas M.
Nefedov, Michael
de Jong, Pieter J.
Lyons, Paul
Wicker, Linda
Todd, John
Hayashizaki, Yoshihide
Gulban, Omid
Danska, Jayne
Harrow, Jen
Hubbard, Tim
Rogers, Jane
Adams, David J.
author_sort Steward, Charles A.
collection PubMed
description Non-obese diabetic (NOD) mice spontaneously develop type 1 diabetes (T1D) due to the progressive loss of insulin-secreting β-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.
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spelling pubmed-28241082010-03-03 Genome-wide end-sequenced BAC resources for the NOD/MrkTac(☆) and NOD/ShiLtJ(☆☆) mouse genomes Steward, Charles A. Humphray, Sean Plumb, Bob Jones, Matthew C. Quail, Michael A. Rice, Stephen Cox, Tony Davies, Rob Bonfield, James Keane, Thomas M. Nefedov, Michael de Jong, Pieter J. Lyons, Paul Wicker, Linda Todd, John Hayashizaki, Yoshihide Gulban, Omid Danska, Jayne Harrow, Jen Hubbard, Tim Rogers, Jane Adams, David J. Genomics Article Non-obese diabetic (NOD) mice spontaneously develop type 1 diabetes (T1D) due to the progressive loss of insulin-secreting β-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. Academic Press 2010-02 /pmc/articles/PMC2824108/ /pubmed/19909804 http://dx.doi.org/10.1016/j.ygeno.2009.10.004 Text en © 2010 Elsevier Inc. https://creativecommons.org/licenses/by/3.0/ Open Access under CC BY 3.0 (https://creativecommons.org/licenses/by/3.0/) license
spellingShingle Article
Steward, Charles A.
Humphray, Sean
Plumb, Bob
Jones, Matthew C.
Quail, Michael A.
Rice, Stephen
Cox, Tony
Davies, Rob
Bonfield, James
Keane, Thomas M.
Nefedov, Michael
de Jong, Pieter J.
Lyons, Paul
Wicker, Linda
Todd, John
Hayashizaki, Yoshihide
Gulban, Omid
Danska, Jayne
Harrow, Jen
Hubbard, Tim
Rogers, Jane
Adams, David J.
Genome-wide end-sequenced BAC resources for the NOD/MrkTac(☆) and NOD/ShiLtJ(☆☆) mouse genomes
title Genome-wide end-sequenced BAC resources for the NOD/MrkTac(☆) and NOD/ShiLtJ(☆☆) mouse genomes
title_full Genome-wide end-sequenced BAC resources for the NOD/MrkTac(☆) and NOD/ShiLtJ(☆☆) mouse genomes
title_fullStr Genome-wide end-sequenced BAC resources for the NOD/MrkTac(☆) and NOD/ShiLtJ(☆☆) mouse genomes
title_full_unstemmed Genome-wide end-sequenced BAC resources for the NOD/MrkTac(☆) and NOD/ShiLtJ(☆☆) mouse genomes
title_short Genome-wide end-sequenced BAC resources for the NOD/MrkTac(☆) and NOD/ShiLtJ(☆☆) mouse genomes
title_sort genome-wide end-sequenced bac resources for the nod/mrktac(☆) and nod/shiltj(☆☆) mouse genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824108/
https://www.ncbi.nlm.nih.gov/pubmed/19909804
http://dx.doi.org/10.1016/j.ygeno.2009.10.004
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