The data consists of gene expression data of F1 crosses between three pairs of Drosophila melanogaster lines from the Drosophila Genetic Reference Panel (DGRP-757 x DGRP-392, DGRP-208 x DGRP-808 and DGRP-83 x DGRP-332). For each pair, we performed both within-line crosses as well as the two between-line reciprocals, and obtained two replicated measures of sex-specific gene expression in heads and gonads for each of the four crosses per pair. We trimmed the demultiplexed data using Trimmomatic and performed UMI-based deduplication using UMI-tools. 

Dataset S1. Overall count data in parentals and hybrids estimated using Kallisto. Each column contains count gene expression for a particular sample. Each sample is labeled as follows: 1 2 3. 1 indicates the maternal (F) and paternal (M) lines of the hybrid cross. 2 is the tissue and sex: fh (female heads), fo (female ovaries), mh (male heads) and mt (male testes). 3 is the replicate: R1 or R2. Expression data for samples 392F x 757M mh R2, 392M x 392F mt R2 and 808M x 208F mt R2 are removed due to low quality, and not used in any analysis. The last two columns (chr and start) are the chromosome and position of the gene.

Dataset S2. Overall TPM data in parentals and hybrids estimated using Kallisto, used in the Dominance estimates. Each column contains TPM gene expression for a particular sample. Each sample is labeled as follows: 1 2 3. 1 indicates the maternal (F) and paternal (M) lines of the hybrid cross. 2 is the tissue and sex: fh (female heads), fo (female ovaries), mh (male heads) and mt (male testes). 3 is the replicate: R1 or R2. Expression data for samples 392F x 757M mh R2, 392M x 392F mt R2 and 808M x 208F mt R2 are removed due to low quality, and not used in any analysis. The last two columns (chr and start) are the chromosome and position of the gene.

Dataset S3. Overall parental and allele-specific hybrid count expression estimated using ASETigar. Each column contains count gene expression for a particular sample. Parental overall expression data has been estimated using the ASETigar pipeline (see Methods) so that the estimates are comparable to the allelic expression in the hybrids. Expression for each specific pairwise comparison is labeled as 1_2_34_5. 1 and 2 are the two lines being compared, 3 is the tissue and sex: fh (female heads), fo (female ovaries), mh (male heads) and mt (male testes), 4 is the replicate: R1 or R2. 5 is the line (corresponding with 1 or 2) for which expression is estimated. Hybrid allele-specific expression estimates are labeled as 1Fx2M_3_4_5. 1 and 2 indicate the maternal and paternal lines of the hybrid cross, respectively. 3 is the tissue and sex, 4 the replicate and 5 the line (corresponding with 1 or 2) for which allele-specific expression is estimated. Expression data for samples 392F x 392M mt R2, 208Fx808M_mt_R2 and 392Fx757M_mh_R2 are removed due to low quality and not used in the analysis. The last two columns (chr and start) are the chromosome and position of the gene. This dataset is used to estimate cis regulatory effects via the two described methods: only hybrid allele-specific expression was used for CR, PO and MG estimates following Takada et al. (2017)’s pipeline; parental and hybrid allelic expression was used for the cis vs trans estimates of regulatory variation following McManus et al. (2010)’s approach.

Dataset S4. Overall parental and allele-specific hybrid FPKM expression estimated using ASETigar. Each column contains FPKM gene expression for a particular sample. Parental overall expression data has been estimated using the ASETigar pipeline (see Methods) so that the estimates are comparable to the allelic expression in the hybrids. Expression for each specific pairwise comparison is labeled as 1_2_34_5. 1 and 2 are the two lines being compared, 3 is the tissue and sex: fh (female heads), fo (female ovaries), mh (male heads) and mt (male testes), 4 is the replicate: R1 or R2. 5 is the line (corresponding with 1 or 2) for which expression is estimated. Hybrid allele-specific expression estimates are labeled as 1Fx2M_3_4_5. 1 and 2 indicate the maternal and paternal lines of the hybrid cross, respectively. 3 is the tissue and sex, 4 the replicate and 5 the line (corresponding with 1 or 2) for which allele-specific expression is estimated. Expression data for samples 392F x 392M mt R2, 208Fx808M_mt_R2 and 392Fx757M_mh_R2 are removed due to low quality and not used in the analysis. The last two columns (chr and start) are the chromosome and position of the gene.