Archaeobotanical samples tested in assay.

<p>Archaeobotanical samples tested in assay.</p

Verification of assay on amplified libraries with shotgun sequencing data.

1<p>As discussed in the methods section, the assay percentages are meant as a guide to compare samples and are not expected to match the absolute values yielded via shotgun sequencing.</p>2<p>The scaled shotgun sequencing results do not include reads without BLAST matches or reads which matched higher taxonomic levels (e.g., eukaryotes or metazoa).</p>3<p><i>N/A</i> indicates the primer set did not fluoresce before the negative control for the sample.</p

Primers for qPCR contamination assay.

<p>Primers for qPCR contamination assay.</p

Directions to interpret qPCR assay data.

<p>Follow the questions in the flowchart to compare the endogenous DNA content of different ancient plant samples. The least contaminated samples are best suited for shotgun sequencing.</p

Taxonomic distribution of non-maize HiSeq 2000 reads from cDNA and DNA sets:

<p>(<b>a</b>) represents cDNA sample 935130, (<b>b</b>) represents cDNA sample 935230, and (<b>c</b>) represents a DNA shotgun sample from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050961#pone.0050961-Bannister1" target="_blank">[25]</a> 100,00 randomly sampled unmapped reads were used to perform BLAST searches and MEGAN was for taxonomic characterization of non-maize reference genome (non-B73) reads.</p

Dominant elements represented in repeat content profiles of cDNA and DNA sequences using RepeatMasker.

<p>Dominant elements represented in repeat content profiles of cDNA and DNA sequences using RepeatMasker.</p

Top 50 exon hits with functional annotation from cDNA (935130 and 935230) HiSeq 2000 maize reads (for a detailed version of the table see Supplementary Table S4).

<p>Top 50 exon hits with functional annotation from cDNA (935130 and 935230) HiSeq 2000 maize reads (for a detailed version of the table see Supplementary <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050961#pone.0050961.s010" target="_blank">Table S4</a>).</p

Kernel and sample information and names.

<p>A total of 6 kernels were utilized for either RNA or DNA extraction only, or co-extracted for DNA and RNA. After nucleic acids were co-extracted, samples were divided into 2 aliquots, and RNA samples were DNase treated and DNA samples were RNase treated (see Methods and Supplementary Methods S1), and labeled with unique sample names.</p

Positive correlation matrix of contig read content from cDNA (935130 and 935230) and DNA [25].

<p>Positive correlation matrix of contig read content from cDNA (935130 and 935230) and DNA <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050961#pone.0050961-Bannister1" target="_blank">[25]</a>.</p

Histogram showing fragment length distribution of maize GS FLX sequence reads from 3 Arizonan DNA (FLX4-6) samples (blue) in comparison to 3 Arizonan cDNA (FLX1-3) samples (red).

<p>Histogram showing fragment length distribution of maize GS FLX sequence reads from 3 Arizonan DNA (FLX4-6) samples (blue) in comparison to 3 Arizonan cDNA (FLX1-3) samples (red).</p