Project description:Sequencing of the most 3' end of mRNAs (3'-Tag-Seq) of 82 wild type strains from the Drosophila Genetic reference Panel (DGRP) during embryogenesis was performed. Three different time points (2-4hrs, 6-8hrs and 10 to 12rs after laying) were assayed. 14 biological replicates were performed from independent embryo collections.
Project description:Chromosome conformation capture (4C-Seq) in Drosophila Twist-H2B embryos (carrying nuclear tag specifically in the mesoderm) during embryogenesis was performed, anchoring on 107 different viewpoints. Two timepoints (3-4hrs and 6-8hrs after egg laying) and two tissue context (whole embryo and mesoderm) were assayed. Two independent collections were performed at each timepoint.
Project description:Drosophila melanogaster is a well-studied genetic model organism with several large-scale transcriptome resources. Here we investigate 7,952 proteins during the fly life cycle from embryo to adult and also provide a high-resolution temporal time course proteome of 5,458 proteins during embryogenesis. We use our large scale data set to compare transcript/protein expression, uncovering examples of extreme differences between mRNA and protein abundance. In the embryogenesis proteome, the time delay in protein synthesis after transcript expression was determined. For some proteins, including the transcription factor lola, we monitor isoform specific expression levels during early fly development. Furthermore, we obtained firm evidence of 268 small proteins, which are hard to predict by bioinformatics. We observe peptides originating from non-coding regions of the genome and identified Cyp9f3psi as a protein-coding gene. As a powerful resource to the community, we additionally created an interactive web interface (http://www.butterlab.org) advancing the access to our data.
Project description:In this study we use a combination of proteomics Label-Free quantification methods to monitor protein expression changes over a time course of more than 20 hours of embryo development in Drosophila melanogaster.
Project description:Sequencing of mRNAs of 22 wild type strains from the Drosophila Genetic reference Panel (DGRP) at embryonic time point 10-12 hrs after egg laying was performed. ~100 embryos were pooled for each biological sample prior to library preparation.
Project description:Chromatin accessibility mapping by DNase-seq on whole embryo and FACS-isolated cell populations during Drosophila melanogaster embryogenesis at 2-4 hrs, 4-6 hrs, 6-8 hrs, 8-10 hrs and 10-12 hrs after egg-laying. Note that the two 8 bases long UMIs clipped from read1 and read2 are present in the FastQ file header (followed by the 8 bp long invariant sample barcode)
Project description:Chromatin accessibility mapping by DNase-seq on FACS-isolated cell populations during Drosophila melanogaster embryogenesis (6-8 hrs after egg-laying)
Project description:Background: The early stages of D. melanogaster embryogenesis involve cell migration and pattern formation, and lead to the formation of three germ layers (the ectoderm, mesoderm and endoderm). These developmental events are controlled by differential gene activity. In the current study we used a suppressive subtractive hybridization (SSH) procedure to identify a group of genes potentially involved in D. melanogaster early embryogenesis and to study the temporal activity of developmentally regulated genes at five different intervals covering 12 stages of embryogenesis. Results: Macroarrays were constructed to confirm induction of expression and determine the temporal profile of isolated subtracted cDNAs during embryo development. We identified a set of 118 genes that significantly increased their expression levels at least at one developmental interval compared with the reference interval. 53.4% of them have a phenotype and/or molecular function reported in the literature, whereas 46.6% are essentially uncharacterized. Clustering analysis revealed demarcated transcript groups with maximum gene activity at distinct developmental intervals. In situ hybridization assays were carried out on 30 of the transcripts and of these, 19 (63%) proved to have restricted expression patterns. 11 of the uncharacterized genes that exhibited temporal and spatially restricted patterns of expression in developing embryos encode putative secreted and transmembrane proteins. For three of them we validated our protein sequence predictions by expressing their cDNAs in S2R+ cells and analyze the subcellular distribution of recombinant proteins. Conclusions: Our data provides a list of developmentally regulated D. melanogaster genes and their expression profiles during embryogenesis, including novel information on the temporal and spatial expression patterns of several previously uncharacterized genes. In particular, we recovered a significant number of novel genes encoding putative secreted and transmembrane proteins, suggesting new components of signalling pathways that might be incorporated within the existing regulatory networks controlling Drosophila embryogenesis; they are also good candidates for more functional targeted analyses. Keywords: Drosophila melanogaster, gastrulation, macroarray, developmental time course