The molecular landscape of neural differentiation inthe developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis

In this work, Michki et. al. isolate neurons and neural progenitors from the developing Drosophila brain. Through a combination of in silico and in situ techniques, they map out the expression dynamics of a variety of molecular factors that may play a role in specifying terminal neural fates at the RNA level, and provide tools to enable similar analyses to be performed in other systems. Overall design: R9D11-Gal4 genetic driver was used with a UAS:hH2B-2xmNG reporter to label type-II neural lineages in third instar larval brains. 20 brains were dissected, dissociated, and sorted on a Sony MA900 FACS machine. 10,000 cells were sequenced in a single lane of a 10Xchromium chip using their v3 chemistry. Cells were sequenced on an Illumina NovaSeq/HiSeq4000 with 400M reads allocated to this library. 6092 cells were identified with a mean read count of 97,604 reads/cell when aligned to the BDGP6(2014-07) Drosophila genome assembly from ENSEMBL using STAR. Downstream filtering and analysis were performed using scanpy.