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Series GSE68062 Query DataSets for GSE68062
Status Public on Apr 21, 2015
Title Sex bias and maternal contribution to gene expression divergence in Drosophila blastoderm embryos
Organisms Drosophila melanogaster; Drosophila pseudoobscura; Drosophila virilis; Drosophila yakuba
Experiment type Expression profiling by high throughput sequencing
Summary Early embryogenesis is a unique developmental stage where genetic control of development is handed off from mother to zygote. Yet the contribution of this transition to the evolution of gene expression is poorly understood. Here we study two aspects of gene expression specific to early embryogenesis in Drosophila: sex-biased gene expression prior to the onset of canonical X chromosomal dosage compensation, and the contribution of maternally supplied mRNAs. We sequenced mRNAs from individual unfertilized eggs, precisely staged and sexed blastoderm embryos and compared levels between D. melanogaster, D. yakuba, D. pseudoobscura and D. virilis. First, we find that mRNA content is highly conserved for a given stage and that studies relying on pooled embryos may systematically overstate the degree of gene expression divergence. Unlike studies done on larvae and adults, where most species show a larger proportion of genes with male-biased expression, we find that transcripts in Drosophila embryos are largely female-biased in all species, likely due to incomplete dosage compensation prior to the activation of the canonical dosage compensation mechanism. The divergence of sex-biased gene expression across species is observed to be often due to a decrease of expression, the most drastic example of which is the overall reduction of male expression from the neo-X chromosome in D. pseudoobscura, leading to a pervasive female-bias on this chromosome. We see no evidence for a faster evolution of expression on the X chromosome in embryos (no “faster X” effect), unlike in adults and contrary to a previous study on pooled non-sexed embryos. Finally, we find that most genes are conserved in regard to their maternal or zygotic origin of transcription, and present evidence that differences in maternal contribution to the blastoderm transcript pool may be due to species-specific divergence of transcript degradation rates
Overall design We sequenced mRNA from D. melanogaser, D. yakuba, D. pseudoobscura and D. virilis single unfertilized eggs (1 to 2 per species) and from both single female and male embryos (3 per sex per species).
Contributor(s) Paris M, Villalta JE, Eisen MB, Lott SE
Citation(s) 26485701
Submission date Apr 20, 2015
Last update date May 15, 2019
Contact name Mathilde Paris
Organization name CNRS
Department IGFL
Street address Faculte des sciences de Luminy, case 907
ZIP/Postal code 69007
Country France
Platforms (4)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
GPL13307 Illumina HiSeq 2000 (Drosophila yakuba)
GPL13310 Illumina HiSeq 2000 (Drosophila pseudoobscura)
Samples (31)
GSM1662140 mel.M.1
GSM1662141 mel.M.2
GSM1662142 mel.M.3
BioProject PRJNA281640
SRA SRP057462

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Supplementary file Size Download File type/resource
GSE68062_Gene_CLASS_after_FPKM_normalization.txt.gz 108.8 Kb (ftp)(http) TXT
GSE68062_Gene_CLASS_after_Q_normalization.txt.gz 109.9 Kb (ftp)(http) TXT
GSE68062_Gene_CLASS_after_TMM_normalization.txt.gz 109.2 Kb (ftp)(http) TXT
GSE68062_Gene_CLASS_after_p50_normalization.txt.gz 108.2 Kb (ftp)(http) TXT
GSE68062_Gene_CLASS_after_p75_normalization.txt.gz 108.3 Kb (ftp)(http) TXT
GSE68062_Gene_CLASS_after_p95_normalization.txt.gz 109.0 Kb (ftp)(http) TXT
GSE68062_Gene_abundances_after_FPKM_normalization.txt.gz 2.4 Mb (ftp)(http) TXT
GSE68062_Gene_abundances_after_Q_normalization.txt.gz 2.3 Mb (ftp)(http) TXT
GSE68062_Gene_abundances_after_TMM_normalization.txt.gz 2.4 Mb (ftp)(http) TXT
GSE68062_Gene_abundances_after_p50_normalization.txt.gz 2.4 Mb (ftp)(http) TXT
GSE68062_Gene_abundances_after_p75_normalization.txt.gz 2.4 Mb (ftp)(http) TXT
GSE68062_Gene_abundances_after_p95_normalization.txt.gz 2.4 Mb (ftp)(http) TXT
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