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Genome-Scale Validation of Deep-Sequencing Libraries

Chromatin immunoprecipitation followed by high-throughput (HTP) sequencing (ChIP-seq) is a powerful tool to establish protein-DNA interactions genome-wide. The primary limitation of its broad application at present is the often-limited access to sequencers. Here we report a protocol, Mab-seq, that g...

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Detalles Bibliográficos
Autores principales: Schmidt, Dominic, Stark, Rory, Wilson, Michael D., Brown, Gordon D., Odom, Duncan T.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577887/
https://www.ncbi.nlm.nih.gov/pubmed/19002256
http://dx.doi.org/10.1371/journal.pone.0003713
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author Schmidt, Dominic
Stark, Rory
Wilson, Michael D.
Brown, Gordon D.
Odom, Duncan T.
author_facet Schmidt, Dominic
Stark, Rory
Wilson, Michael D.
Brown, Gordon D.
Odom, Duncan T.
author_sort Schmidt, Dominic
collection PubMed
description Chromatin immunoprecipitation followed by high-throughput (HTP) sequencing (ChIP-seq) is a powerful tool to establish protein-DNA interactions genome-wide. The primary limitation of its broad application at present is the often-limited access to sequencers. Here we report a protocol, Mab-seq, that generates genome-scale quality evaluations for nucleic acid libraries intended for deep-sequencing. We show how commercially available genomic microarrays can be used to maximize the efficiency of library creation and quickly generate reliable preliminary data on a chromosomal scale in advance of deep sequencing. We also exploit this technique to compare enriched regions identified using microarrays with those identified by sequencing, demonstrating that they agree on a core set of clearly identified enriched regions, while characterizing the additional enriched regions identifiable using HTP sequencing.
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spelling pubmed-25778872008-11-12 Genome-Scale Validation of Deep-Sequencing Libraries Schmidt, Dominic Stark, Rory Wilson, Michael D. Brown, Gordon D. Odom, Duncan T. PLoS One Research Article Chromatin immunoprecipitation followed by high-throughput (HTP) sequencing (ChIP-seq) is a powerful tool to establish protein-DNA interactions genome-wide. The primary limitation of its broad application at present is the often-limited access to sequencers. Here we report a protocol, Mab-seq, that generates genome-scale quality evaluations for nucleic acid libraries intended for deep-sequencing. We show how commercially available genomic microarrays can be used to maximize the efficiency of library creation and quickly generate reliable preliminary data on a chromosomal scale in advance of deep sequencing. We also exploit this technique to compare enriched regions identified using microarrays with those identified by sequencing, demonstrating that they agree on a core set of clearly identified enriched regions, while characterizing the additional enriched regions identifiable using HTP sequencing. Public Library of Science 2008-11-12 /pmc/articles/PMC2577887/ /pubmed/19002256 http://dx.doi.org/10.1371/journal.pone.0003713 Text en Schmidt et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Schmidt, Dominic
Stark, Rory
Wilson, Michael D.
Brown, Gordon D.
Odom, Duncan T.
Genome-Scale Validation of Deep-Sequencing Libraries
title Genome-Scale Validation of Deep-Sequencing Libraries
title_full Genome-Scale Validation of Deep-Sequencing Libraries
title_fullStr Genome-Scale Validation of Deep-Sequencing Libraries
title_full_unstemmed Genome-Scale Validation of Deep-Sequencing Libraries
title_short Genome-Scale Validation of Deep-Sequencing Libraries
title_sort genome-scale validation of deep-sequencing libraries
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577887/
https://www.ncbi.nlm.nih.gov/pubmed/19002256
http://dx.doi.org/10.1371/journal.pone.0003713
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