ChIP-Seq on adults of S.mansoni SmBRE from sympatric snail hosts- Adulte_Bre_Fa_1_H3K4me3
ChIP products were sequenced as single-end 50 bp reads on an Illumina HiSeq 2500 at the McGill University and Génome Québec Innovation Centre (http://gqinnovationcenter.com/index.aspx). Briefly, fragmented DNA was quantified using 2100 Bioanalyzer (Agilent Technologies). Libraries were generated robotically with 10 ng of fragmented DNA (range 100-300 bp) using the Kapa HTP Library Preparation Kit (Kapa Biosystems) as per the manufacturer’s recommendations except that adapters and PCR primers were diluted 100-fold. The size selection step was done after the PCR step and the number of PCR cycles increased by 6. Adapters and PCR primers were purchased from Integrated DNA Technologies) whereas size selection has been performed on a Pippin Prep instrument (SAGE Biosciences Inc). Libraries were quantified using the Quant-iT™ PicoGreen® dsDNA Assay Kit (Life Technologies) and the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (D-Mark). Average size fragment was determined using a LabChip GX (PerkinElmer) instrument. Cluster formation on the flow cell was performed using the cBot instrument (Illumina) with four indexed libraries per lane. Sequencing, in the form of 50-cycle single end reads, was performed on a HiSeq 2000/2500 (Illumina) running HCS software version 2.2.38. Demultiplexed FASTQ files were generated by allowing up to one mismatch in the index.