Instrument: Illumina Genome Analyzer IIx
Strategy: FAIRE-seq
Source: GENOMIC
Selection: other
Layout: SINGLE
Construction protocol: FAIRE was performed as described (Giresi et al. 2007; Giresi and Lieb 2009) DNA fragments are prepped for sequencing using the recommended protocol except that samples are amplified prior to gel extraction. Adaptor-ligated DNA fragments amplified using PCR and ranging from 150 to 400 bp were subsequently purified from agarose gels (Qiagen Gel Extraction kit). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~150-400 bp were isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.