Supporting Information
Tables S1-S8.
P-values from homoscedastic variance t -tests (implemented in JMP) were performed to evaluate tissue-specific and genotype-specific patterns of expression bias. Significant p-values are indicated in bold.
Supplemental files S9-S15 . Raw data generated from 454 sequencing of amplicons from various hybrid tissues. Read counts for each allele are indicated in columns C and D. The genomic control ratio is in column F. Normalized ratios are in column G. P-values are in column N. Five letter nucleotide codes indicating hybrid designations (column A) are as follows: Hybrid 1: AT--- = D4201xD4202; TA--
- = D4202xD4201; Hybrid 2: GC--- = D4204 x D4205; CG--- = D4205 x D4202;
Hybrid 3: GT--- = D4204 x D5156; TG--- = D5156 x D4204; Hybrid 4: AT--- = D4205 x D4202; TA--- = D4202 x D4205. The third nucleotide indicates tissue type, where -
-A-- = leaf, --T-- = root, --G-- = ear, and --C-- = tassel. The fourth nucleotide in the code designates the sample type where ---C- = cDNA, and ---G- = genomic DNA.
The last nucleotide position in the code was used to distinguish between replicates, and where the same nucleotide is used, the replicates were sequenced on the
Roche 454 machine during separate runs.
Supplemental file S16. Raw data generated from 454 sequencing of Tac7077 amplicons from various hybrid tissues. Because sequencing of the biological replicates failed for this gene, we were unable to pool replicates for homoscedastic variance t -tests. Binomial distributions and percent error are shown. Five letter nucleotide code designations are identical to that for Supplemental files S9-S15.

Supplemental files S17-S23.
Percent error calculations for biological samples and their technical replicates. Normalized ratios are shown in column G. Percent error is indicated in column H. Five letter nucleotide code designations are identical to that for Supplemental files S9-S15.