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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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2008-01-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0003713&type=printable |
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| _version_ | 1850183023653289984 |
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| author | Dominic Schmidt Rory Stark Michael D Wilson Gordon D Brown Duncan T Odom |
| author_facet | Dominic Schmidt Rory Stark Michael D Wilson Gordon D Brown Duncan T Odom |
| author_sort | Dominic Schmidt |
| collection | DOAJ |
| 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. |
| format | Article |
| id | doaj-art-86c1d64b82f54441b80fc8adca11bc72 |
| institution | OA Journals |
| issn | 1932-6203 |
| language | English |
| publishDate | 2008-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-86c1d64b82f54441b80fc8adca11bc722025-08-20T02:17:28ZengPublic Library of Science (PLoS)PLoS ONE1932-62032008-01-01311e371310.1371/journal.pone.0003713Genome-scale validation of deep-sequencing libraries.Dominic SchmidtRory StarkMichael D WilsonGordon D BrownDuncan T OdomChromatin 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.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0003713&type=printable |
| spellingShingle | Dominic Schmidt Rory Stark Michael D Wilson Gordon D Brown Duncan T Odom Genome-scale validation of deep-sequencing libraries. PLoS ONE |
| 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 |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0003713&type=printable |
| work_keys_str_mv | AT dominicschmidt genomescalevalidationofdeepsequencinglibraries AT rorystark genomescalevalidationofdeepsequencinglibraries AT michaeldwilson genomescalevalidationofdeepsequencinglibraries AT gordondbrown genomescalevalidationofdeepsequencinglibraries AT duncantodom genomescalevalidationofdeepsequencinglibraries |