High-resolution gene expression data from blastoderm embryos of the scuttle fly Megaselia abdita

Abstract

Gap genes are involved in segment determination during early development in dipteran insects (flies, midges, and mosquitoes). We carried out a systematic quantitative comparative analysis of the gap gene network across different dipteran species. Our work provides mechanistic insights into the evolution of this pattern-forming network. As a central component of our project, we created a high-resolution quantitative spatio-temporal data set of gap and maternal co-ordinate gene expression in the blastoderm embryo of the non-drosophilid scuttle fly, Megaselia abdita. Our data include expression patterns in both wild-type and RNAi-treated embryos. The data-covering 10 genes, 10 time points, and over 1,000 individual embryos-consist of original embryo images, quantified expression profiles, extracted positions of expression boundaries, and integrated expression patterns, plus metadata and intermediate processing steps. These data provide a valuable resource for researchers interested in the comparative study of gene regulatory networks and pattern formation, an essential step towards a more quantitative and mechanistic understanding of developmental evolution.

Figure 1. Overview of data records presented in this paper.

(a) Data Records 1 (wild-type) and 2 (RNAi). These data records include cropped and rotated images of gap gene expression taken using bright field and differential interference contrast optics (ch00 and dic_ch00 suffixes respectively), an image of the nuclear counterstain (nuc_ch00) and an unprocessed image of the dorsal membrane morphology (memb_ch00). These data records also include embryo masks (embmask) and images of the band location superimposed onto the embryo mask (band) and brightfield (stband) images. The file 001_ch00_prof.dat contains averaged band RGB values seen plotted in magenta in (b). (b) Data Records 3 (wild-type) and 4 (RNAi): these records are composed of two CSV files that document the time class and position of the 10% strip used for profile extraction for each embryo (File 1), plus the associated boundary IDs and coordinates (File 2). The graph shows an example, where splines fit to boundaries 2, 5, 6 and 7 of gt are plotted against the extracted profile (magenta; see Fig. 2 for boundary numbers). Images in (a) and (b) correspond to embryo 001 that can be found in Data Record 1 in ish/megaselia/ma_gt_260911/proc. (c) Data Record 5. This data record is composed of a CSV file containing averaged coordinates and standard deviations of expression boundaries for each gene. Embryos are oriented with anterior to the left, dorsal up.

Figure 2. M. abdita boundary naming scheme.

This figure displays schematic drawings of embryos showing expression boundary numbers and relative positions for each M. abdita gene listed in File 2 of Data Records 3 and 4. gt boundaries 3 and 4 are omitted to provide consistent numbering with homologous D. melanogaster boundaries. Maternal inputs (bcd, cad) and terminal gap genes (tll, hkb) are shown on the left. Trunk gap genes (hb, Kr, gt, kni) are shown on the right. Embryos drawn anterior to the left, dorsal up. Figure reproduced from (ref. , Supplementary File 2).