whole genome sequencing of Adelie penguin ancient sample: Sample CB070117.03
"Ancient Adelie penguin samples (ages determined as described in (Subramanian et al. 2009)) were prepared in a physically isolated laboratory utilized only for aDNA work, following strict guidelines to minimize the chance of contamination (i.e., unidirectional daily traffic from aDNA to modern DNA facilities, positive air pressure, frequent decontamination of working surfaces with bleach and alcohol solutions, dedicated foot-, body-, face- and headwear). DNA was extracted from bone shavings using an EDTA/proteinase K digestion for 12-18 hours at 55 C followed by organic extraction with ultra-pure buffer-saturated phenol and chloroform (Sigma-Aldrich, St. Louis, MO, USA) and purification with Qiagen MinElute or PCR Purification columns utilizing high concentration buffer PB (10:1 buffer:sample volume ratio) to avoid loss of small fragments. Purified extractions were then built into libraries following the protocol of Meyer and Kircher (2010) with slight modifications. Designated blank samples were also carried through the entire DNA extraction and library preparation process alongside ancient samples, at a minimum ratio of one blank for every eight samples. Finished library yield was checked on all samples using the Agilent 2100 BioAnalyzer (HSDna Kit) (Agilent, Santa Clara, CA, USA), and any group of samples showing library yield in their associated blank was discarded. Finished libraries were purified using Qiagen MinElute columns or Axygen MAG-PCR SPRI beads (Corning Life Sciences, Tewksbury, MA, USA) at a ratio of 0.7-0.8:1 Axygen:sample volume to remove adapter dimers, and quantified with a Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY, USA). Libraries were submitted for 101bp single-end (SE) sequencing on an Illumina HiSeq2000 either to BGI-Hong Kong or the National High-Throughput Sequencing Center (University of Denmark, http://seqcenter.ku.dk/)."