Gene expression profile at single embryo level of 0-3h old hybrid Drosophila embryos

We used single-embryo RNA-sequencing (RNA-seq) to characterize early zygotic gene expression in Drosophila. To assess the accurate transcriptional activation for zygotic genes, we analyze the paternal allele expression as embryos initially contain trace amounts of paternal mRNAs delivered by the sperm. For this purpose, we used two genetically different lines from the Drosophila Genetic Reference Panel (DGRP) with known genetic variations in our crosses (males/DGRP_352, females/DGRP_737). The data provide a continuous timeline of transcript levels and allele-specific gene expression during early development (≤ 3 hours) in Drosophila melanogaster. Deposited RNA-seq data is part of a multi-'omics approach and prior metabolite extraction was performed in each sample. RNA from single Drosophila embryos was isolated and used for library preparation by a modified CelSeq2 single-cell RNA-seq protocol. Next, we performed pseudo-temporal analysis on the single-embryo RNA-seq data to get a high-resolution, time-resolved picture of transcriptional events during early embryonic development. To get allele-specific gene expression, we performed variant calling on the hybrid offspring by a modified GATK’s workflow retaining only known and biallelic SNPs annotated to a single gene. Finally, we match our pseudo-time analysis with the allele-specific gene expression in each embryo. Note: the normalized reads in pseudo-time order that are provided as supplementary file include 8 unfertilized eggs (prefix U) which should be excluded when exclusively analyzing embryo development (n=245 embryos, prefix E).