title: UluPandan October gDNA Illumina HiSeq 2000 runs
design: Extracted DNA from the October samples was sheared on a Covaris S2 instrument to 300bp following the manufacturers recommendation. For each sample, 2.5 μg of DNA was used in a total volume of 120 μL of TE buffer. The sheared DNA samples were subjected to Illumina paired-end library preparation using a Beckman SPRIworks Fragment Library System and Beckman Fragment Library Kit I reagents. Ten microliters of PE Adapter Oligo Mix (Illumina) were loaded onto the instrument for each sample. Library preparation was performed according to the pre-programmed Illumina library preparation method. Size-selection on the SPRIworks was skipped and performed separately after PCR amplification. After library preparation, samples were removed from the SPRIworks and quantitated using Picogreen fluorescent dye (Invitrogen). The concentration of each library was normalized to 10 μg/μL. For each library, 4 independent PCR reactions were set-up consisting of the following components: 1 μL of normalized library, 0.5 μL of PCR PE Primer 1.0 (Illumina), 0.5 uL of PCR PE Primer 2.0 (Illumina), 23 μL of water, and 25 μL of 2x Phusion PCR Master Mix  (Finnzymes). Libraries were amplified for 7 cycles using the following cycling parameters:     1=  98°C 0:30     2= 98°C 0:10     3= 65°C 0:30     4= 72°C 0:30     5= Goto 2 repeat 7x     6= 72°C 3:00     7= 10°C  Hold  After amplification, the 4 PCR reactions for each library were pooled, purified on a PCR Purification column (Qiagen), and eluted in 30 μL of buffer EB (Qiagen). Amplified libraries were size-selected on a Pippin Prep instrument (Sage Science) by using a 2% agarose cassette with ethidium bromide. Sizing was performed by selecting a narrow peak at 370bp +/-10%.