Fig. 3

Primary, fixed cells from dissociated Drosophila embryos cluster into distinct cell populations. Drosophila embryos were collected in 2-h time periods, aged for 6 h, dissociated into single cells and fixed. Drop-seq data correspond to two independent embryo collections, with three and four technical replicates, respectively. Libraries were sequenced to a median depth of ~13,250 aligned reads per cell. Cells expressing fewer than 1000 UMIs were excluded from the analysis. a Distribution and the median of the number of genes and transcripts (UMIs) detected per cell in Drop-seq data pooled from seven Drop-seq runs, representing a total of 4873 cells. Note that violin plots are displayed on a log scale. b Clustering of 4873 fixed cells into distinct cell populations. The plot shows a two-dimensional representation (tSNE) of global gene expression relationships among all cells. Tissue associations were made by ImaGO term analysis [20] on the 50 most variable genes of each cluster (Additional file 5: Table S1), followed by inspection of publicly accessible RNA in situ staining patterns. LVM longitudinal visceral musculature. c Marker gene expression in clusters of Drosophila embryo cells (see text for explanations). Expression coloured based on normalized expression levels