A Cell Atlas of the Drosophila ovary

Single-cell RNA sequencing of adult Drosophila ovary using the 10X platform. Ovaries were dissociated to single cells and Single-cell libraries were generated for 435 cells (dataset1), 8326 cells (dataset2) or 5412 cells (dataset3). Cells were sequenced at a depth of~540,000 reads per cell (dataset1), ~40,000 reads per cell (dataset2) or ~ 70,000 reads per cell (dataset3). We identified transcriptomes of 26 distinct cell populations including the stem cells of the germline and the follicle cell lineage as well as three distinct subtypes inner germarial sheath cells, polar cells, stalk cells and subpopulations of main body follicle cells. Single-cell RNA sequencing of adult ovaries (dataset1: 109-30-Gal4/+; 13CO6-GFP/UAS-CD8::GFP, dataset2 and dataset3: Canton-S)using the 10X platform and HiSeq2500. Live cells were dissociated and run on 1 well of the 10X instrument using the Chromium Single Cell 3' Reagent Version 2 Kit. For dataset1, cells were subjected to MACS prior to loading onto the 10X chip.