A characterization of the diverse populations of hemocytes in the hemolymph of third instar Drosophila larvae, in control conditions and upon infestation by Leptopilina boulardi.
For each condition, single-cell RNA-seq libraries were prepared from 10,000 cells using the Chromium Single Cell 3' Reagent Kits v2 (10x Genomics).
RNA-seq libraries were sequenced on the Illumina HiSeq 4000 platform with paired-end 100 bp reads.
Reads were processed using Cell Ranger v3.0.1 (10x Genomics). They were mapped to the Drosophila melanogaster reference genome BDGP6_ens95. For quality filtering, cells with less than 200 UMI were removed. Further analysis was performed using Seurat v3 (https://satijalab.org/seurat/). Dimensionality reduction and clustering were performed by computing 20 principal components and with a clustering resolution of 0.55.
The EMBL-EBI's Single Cell Expression Atlas provides cell-level annotations, clustering data, raw and normalised read counts, and putative marker genes.
