A characterization of the diverse populations of cells in the wing disc of third instar Drosophila larvae, with a focus on the precursors to flight muscles and the role of Amalgam in muscle differentiation.
Single-cell RNA-seq libraries were prepared using the DROP-seq method (Macosko et al., 2015).
RNA-seq libraries were sequenced on the Illumina NextSeq platform.
Reads were processed using the Dropseq-tools v1.13 following the Drop-seq Core Computational Protocol v1.2. They were mapped to the Drosophila melanogaster reference genome BDGP6. Further analysis was performed using Seurat v3.0.0. For quality filtering, cells with less 200 genes or more than 2,500 genes were excluded, as well as cells with more than 10% of mitochondrial genes, more than 6% of HSP genes, or more than 1.5% of 28sRNA. For dimensionality reduction, principal component analysis was performed using the top 2,000 variable genes, and the first 30 principal components were selected as input for Uniform Manifold Approximation and Projection (UMAP) clustering.
The EMBL-EBI's Single Cell Expression Atlas provides cell-level annotations, clustering data, raw and normalised read counts, and putative marker genes.
