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Chromatin immunopreciptiation of mouse hepatocytes to validate deep-sequencing libraries

ABSTRACT: Chromatin immunoprecipitation followed by ultra-high throughput (UHTP) sequencing (ChIP-seq) is a powerful tool to establish protein-DNA interactions genome-wide, and the primary limitation of its broad application at present is the often-limited access to sequencers. Here, we report a protocol, Mab-Seq, to generate preliminary quality evaluations and single-chromosome data for deep-sequencing libraries. We show that commercially available genomic microarrays can be used to maximize the efficiency of library creation, quickly generate preliminary data on a chromosomal scale, and help establish the depth to which novel libraries will require deep sequencing.

ORGANISM(S): Mus musculus

SUBMITTER: Dominic Schmidt

PROVIDER: E-TABM-485 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-scale validation of deep-sequencing libraries.

Schmidt Dominic D Stark Rory R Wilson Michael D MD Brown Gordon D GD Odom Duncan T DT

PloS one 20081112 11

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 libr ...[more]

PMID: 19002256

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