Illumina lane 1: nasal swab samples from patients with 2009 pandemic influenza infection (multiplexed)
Libraries for deep sequencing were prepared from amplified cDNA libraries using previously published protocols (Sorber, Chiu, et al, 2008, PloS One).  Briefly, libraries were cleaved with Type IIs restriction endonucleases (GsuI), and truncated adapters containing unique 3 or 6 bp molecular barcodes were ligated on the resulting strand ends.  Full-length adapters were subsequently added via an additional 15 to 25 cycles of PCR.  Libraries were size-selected on a 4% polyacrylamide gel at approximately 350 bp average length, and then loaded at a final concentration of 10 pM on three lanes of a second-generation Genome Analyzer IIx (Illumina, San Diego, CA).  Paired-end reads were sequenced for 67 cycles in each direction. Submitter filtered to remove contaminating human sequences.