Single cell RNA-seq of Drosophila gastrula by using Fluidigm C1 HT

During embryogenesis, cells divide and get different fates to each other. In the process of cell differentiation, cells initiate to express a specific set of transcription factors according to positional information. Then, they show different behavior to drive morphogenesis. To address how cell-type-specific transcriptome pattern controls their behavior for coordinated multicellular tissue morphogenesis, it is important to obtain data on genome-wide gene expression profiles at the single-cell resolution. In this project, We performed a scRNA-seq analysis of Drosophila gastrula exhibiting dynamic morphogenetic movements. Overall design: scRNA-seq data for whole Drosophila embryos at stage 6-7 were collected using the Fluidigm C1 mRNA-seq HT system. This project also includes bulk RNA-seq data for whole embryos, the population of dissociated cells and the population of CellCover-fixed dissociated cells at same developmental stage. These bulk RNA-seq data were used to validate the cell dissociation and fixation methods.