Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq of Drosophila melanogaster neurons, glia and hemocytes at embryonic stage 16 and third instar wandering larvae

ABSTRACT: We produced bulk RNA sequencing data on Drosophila neurons, glia and hemocytes at embryonic and larval stages to extrapolate the most significant and specific features that identify a cell type as a whole. We also tracked changes in the expression in the two stages. We identified stable features that define a cell type functionally and developmentally as well as plastic features including stage-specific metabolic states, which likely depend on the environment.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Rosy Sakr

PROVIDER: E-MTAB-14413 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:An important but largely unmet challenge in understanding the mechanisms that govern formation of specific organs is to decipher the complex and dynamic genetic programs exhibited by the diversity of cell types within the tissue of interest. Here, we use an integrated genetic, genomic and computational strategy to comprehensively determine the molecular identities of distinct myoblast subpopulations within the Drosophila embryonic mesoderm at the time that cell fates are initially specified. A compendium of gene expression profiles was generated for primary mesodermal cells purified by flow cytometry from appropriately staged wild-type embryos and from twelve genotypes in which myogenesis was selectively and predictably perturbed. A statistical meta-analysis of these pooled datasetsâ??based on expected trends in gene expression and on the relative contribution of each genotype to the detection of known muscle genes ?provisionally assigned hundreds of differentially expressed genes to particular myoblast subtypes. Whole embryo in situ hybridizations were then used to validate the majority of these predictions, thereby enabling true positive detection rates to be estimated for the microarray data. This combined analysis reveals that myoblasts exhibit much greater gene expression heterogeneity and overall complexity than was previously appreciated. Moreover, it implicates the involvement of large numbers of uncharacterized, differentially expressed genes in myogenic specification and subsequent morphogenesis. These findings also underscore a requirement for considerable regulatory specificity for generating diverse myoblast identities. Finally, to illustrate how the developmental functions of newly identified myoblast genes can be efficiently surveyed, a rapid RNA interference assay that can be scored in living embryos was developed and applied to selected genes. This integrated strategy for examining embryonic gene expression and function provides a substantially expanded framework for further studies of this model developmental system.

Dataset Information

RNA-seq of Drosophila melanogaster neurons, glia and hemocytes at embryonic stage 16 and third instar wandering larvae

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