This dataset is supplementary to the following manuscript: Svetlana Surkova, Alena Sokolkova, Konstantin Kozlov, Sergey V. Nuzhdin and Maria Samsonova (2019). Quantitative analysis reveals genotype- and domain- specific differences between mRNA and protein expression of segmentation genes in Drosophila. Developmental Biology, doi: 10.1016/j.ydbio.2019.01.006. The archive contains recently obtained quantitative data on expression of eve, gt and hb in Drosophila early embryo at the level of mRNA and protein. It also includes integrated expression profiles of these genes, combined with the prior datasets (Surkova et al., 2008, Surkova et al., 2013). Embryos are classified into 8 time classes within cleavage cycle 14A. Genotype is specified as “wt” (wild type), “het” (Kr+/Kr- heterozygotes) and "mut" (Kr null mutants). Stained channels: EHG (eve mRNA, hb mRNA, gt mRNA); GGE (gt mRNA, Gt protein, eve mRNA); GE (gt mRNA, eve mRNA); ghe (gt mRNA, Hb protein, eve mRNA); HHE (Hb protein, hb mRNA, eve mRNA); GHH (gt mRNA, Hb protein, hb mRNA). The data are arranged in three folders: 1. QData_norm Includes coordinates and fluorescence intensities of segmented nuclei for each individual embryo after subtraction of non-specific background signal. Files are arranged according to time class (T1-T8) and named according to the following scheme: <stained channel><number>_norm.txt Structure of data file: A-P-coord | D-V-coord | channel 1 | channel 2 | channel 3 2. QData_registered Registered one-dimensional gene expression profiles. Files are arranged according to time class (T1-T8) and named according to the following scheme: <stained channel><number>_reg.txt Structure of data file: Number | A-P-coord | channel 3 | channel 2 | channel 1 3. Integrated_data Integrated one-dimensional profiles of eve, hb and gt expression at mRNA and protein levels for wild type embryos, Kr mutants and Kr+/Kr- heterozygotes. eve and gt profiles were normalized on stripe 1 and second anterior domain respectively (see "Materials and Methods)". Files are named according to the following scheme: <gene><genotype><gene product><time class>_100 Structure of data file: Number | A-P coord of an averaged nucleus | averaged intensity hb profiles are named according to the following scheme: <gene><genotype><gene product><time class> Structure of data file: Number | A-P coord of an averaged nucleus | averaged intensity | standard deviation References Surkova S., Kosman D., Kozlov K., Myasnikova E., Samsonova A.A., Spirov A., Vanario-Alonso C.E., Samsonova M., Reinitz J. (2008). Characterization of the Drosophila segment determination morphome. Developmental biology 313(2):844-862. Surkova S., Golubkova E., Manu, Panok L., Mamon L., Reinitz J., Samsonova M. (2013) Quantitative dynamics and increased variability of segmentation gene expression in the Drosophila Kruppel and knirps mutants (2013). Dev Biol. 376: 99-112. doi: 10.1016/j.ydbio.2013.01.008.