title: Illumina sequencing of Mouse HNF4A genomic fragment library
design:  Hepatocytes were purified from mouse liver. The cells were crosslinked with formaldehyde treatment and chromatin fragmented to an average of 300 bp by sonication. Chromatin from 1/3 mouse liver was used for each ChIP experiment. Solexa libraries were prepared following the instructions of Illumina (Sample preparation for genomic DNA version 2.2) with the following modifications. The ChIP-enriched DNA and input DNA were not further fragmented. After end-repair and addition of an A base to the 3prime ends, the adapters were ligated to the ends of the DNA Fragments using 2 ul of  Adapter oligo mix in a total reaction volume of 25 ul. Between these steps, the DNA was purified using the DNA Clean and Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with QIAquick PCR purification Kit, and eluted with 33.5 ul of 10 mM tris buffer at pH7.0. The PCR-product was sized fractionated on 2 percent agarose gel and a gel slice containing the 200-300 bp fragments was excised. The flowcells were prepared and processed according to manufacturer protocols, with single-end sequencing for 36 cycles.         