title: Quercus muehlenbergii Engelm. shotgun genomic sequencing: Sample IL-SH-57
design: "DNA was extracted from leaves or cambium of 97 Quercus species using either the FastDNA Plant kit (MP Bio, Santa Ana, California, USA), or the DNeasy Plant kit (QIAGEN GmbH, Dusseldorf, Germany). DNAs were converted into indexed libraries by using 0.5 ug of total genomic DNA and Illumina TruSeq version 2.0 chemistry (TruSeq DNA sample preparation kit; Illumina, San Diego, California, USA). Final PCR enrichment steps used 12 cycles, rather than the recommended 15 cycles. Indexed samples were pooled into equimolar mixtures containing 24 indices per pool (a 24-plex) and a final concentration of 10 pM. For cluster generation, 11 pmol of sample was loaded into flow cells, and the samples were sequenced using Illumina version 3.0 chemistry for 100 cycles on an Illumina HiSeq 2000 (Oregon State University Center for Genome Research and Biocomputing, Corvallis, Oregon, USA). Sequences were base-called and demultiplexed using Illumina's Consensus Assessment of Sequence and VAriation (CASAVA) software package."