Single-cell transcriptome analysis in D. discoideum (AX4) in different developmental stages
The goal of scRNA-seq is to identify the differential expressed genes in the wild-type D. discoideum at different developmental stages (vegetative, streaming, slug and fruiting bodies). Three biological replicates were assigned for each group and in total 12 groups were prepared for scRNA-seq libraries with 10000 cells as starting materials using Chromium Single Cell Gene Expression kit V3 (10x Genomics). Each sample was sequenced to an average of 393 million reads per sample with Illumina Hiseq 4000 and Novaseq 6000 platforms. The raw fastq files were processed by Cell Ranger (v 3.1.0, all with default setting except --normalize=none for aggr function) to generate the cell-barcode matrix. All downstreaming analysis was performed on R (3.6.3). Seurat package (3.1.5) was mainly used for basic analysis. Slingshot package was use for pseudotime analysis. Overall design: Cells from vegetative, streaming, mound and fruiting body stages were isolated and scRNAseq libraries were generated for deep sequencing, in duplicate, using Hiseq4000 and Novaseq6000.