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 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.
Schmidt
Dominic
D
Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK.
Stark
Rory
R
Wilson
Michael D
MD
Brown
Gordon D
GD
Odom
Duncan T
DT
D047369:Chromatin Immunoprecipitation; D016678:Genome; D015698:Genomic Library; D023281:Genomics / Q000379:methods*; D006801:Humans; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis