REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-Prospero (1:20 dilution)	Developmental Studies Hybridoma Bank	Cat# MR1A; RRID: AB_528440
Rat monoclonal anti-elav (1:100 dilution)	Developmental Studies Hybridoma Bank	Cat# 7E8A10; RRID: AB_528218
Mouse monoclonal anti-Pdf (1:50 dilution)	Developmental Studies Hybridoma Bank	Cat# PDF C7; RRID: AB_760350, AB_2315084
Mouse monoclonal anti-Bruchpilot (1:50 dilution)	Developmental Studies Hybridoma Bank	Cat# nc82; RRID: AB_2314866
Rabbit polyclonal anti-GFP (1:1000 dilution)	Life Technologies	Cat# A-6455; RRID: AB_221570
Donkey polyclonal anti-rabbit Alexa Fluor 488 (1:1000 dilution)	Life Technologies	Cat# A-21206; RRID: AB_2535792
Donkey polyclonal anti-mouse Alexa Fluor 555 (1:1000 dilution)	Life Technologies	Cat# A-31570; RRID: AB_2536180
Goat polyclonal anti-rat Alexa Fluor 647 (1:1000 dilution)	Life Technologies	Cat# A-21247; RRID: AB_141778
Critical Commercial Assays
Acridine Orange/Propidium Iodide Stain	Logos Bio	Cat# F23001
Chromium Single Cell 3′ Library & Gel Bead Kit v2	10x Genomics	Cat# PN-120237
Chromium Single Cell A Chip Kit	10x Genomics	Cat# PN-120236
Chromium i7 Multiplex Kit	10x Genomics	Cat# PN-120262
Nuclei Isolation Kit: Nuclei EZ Prep	Sigma	Cat# NUC101-1KT
Nextera DNA Library prep kit	Illumina	Cat# FC-121-1030
RNAqueous-Micro Total RNA Isolation Kit	ThermoFisher	Cat# AM1931
Dynabeads mRNA Purification Kit	ThermoFisher	Cat# 61006
TruSeq Stranded mRNA Library Prep	Ilumina	Cat# 20020595
MEGAscript T7 Transcription Kit	ThermoFisher	Cat# AM1333
Deposited Data
Raw and analyzed data	This paper	GEO: GSE107451
Lamina/Photoreceptor RNA-seq	Tan et al., 2015	GEO: GSE68235
T4/T5 Neuron RNA-seq	Pankova and Borst, 2016	GEO: GSE77198
α/β/γ Kenyon Cells and Mushroom Body output neurons RNA-seq	Crocker et al., 2016	GEO: GSE74989
Clock Neuron RNA-seq	Abruzzi et al., 2017	GEO: GSE77451
Surface Glia Microarray	DeSalvo et al., 2014	GEO: GSE45344
Olfactory Projection Neuron scRNA-seq	Li et al., 2017	GEO: GSE100058
Optic lobe scRNA-seq	Konstantinides et al., 2018	GEO: GSE103771
Experimental Models: Organisms/Strains
D. melanogaster: DGRP-551	Bloomington Drosophila Stock Center	BDSC: 55026; FlyBase: FBsn0000297
D. melanogaster: w[1118]	Bloomington Drosophila Stock Center	BDSC: 3605; FlyBase: FBal0018186
D. melanogaster: R32E10-Gal4: w[1118]; P{y[+t7.7] w[+mC] = GMR23E10-GAL4}attP2	Bloomington Drosophila Stock Center	BDSC: 49302; FlyBase: FBti0133973
D. melanogaster: Imp-GFP: y[1]w[∗] Mi{PT-GFSTF.2}Imp[MI05901-GFSTF.2]	Bloomington Drosophila Stock Center	BDSC: 60237; FlyBase: FBti0178481
D. melanogaster: OK371-Gal4: w[1118]; P{w[+mW.hs] = GawB}VGlut[OK371]	Bloomington Drosophila Stock Center	BDSC: 26160; FlyBase: FBti0076967
D. melanogaster: AMMC-A1-Gal4: w[∗]; P{w[+mW.hs] = GawB}c767	Bloomington Drosophila Stock Center	BDSC: 30848; FlyBase: FBti0072281
D. melanogaster: GH146-Gal4: y[1] w[1118]; P{w[+mW.hs] = GawB}GH146	Bloomington Drosophila Stock Center	BDSC: 30026; FlyBase: FBti0016783
D. melanogaster: pros-GFP: w[1118]; PBac{y[+mDint2]w[+mC] = pros-GFP.FPTB}VK00037	Bloomington Drosophila Stock Center	BDSC: 66463; FlyBase: FBti0150306
D. melanogaster: pdf-Gal4: y[1] w[∗]; P{w[+mC] = Pdf-GAL4.P2.4}2	Bloomington Drosophila Stock Center	BDSC: 6900; FlyBase: FBti0027914
D. melanogaster: UAS-CD8::GFP: y[1] w[∗]; P{w[+mC] = UAS-mCD8::GFP.L}LL5, P{UAS-mCD8::GFP.L}2	Bloomington Drosophila Stock Center	BDSC: 5137; FlyBase: FBti0180511
D. melanogaster: UAS-mitoTimer: w[1118]; P{w[+mC] = UAS-MitoTimer}3	Bloomington Drosophila Stock Center	BDSC: 57323; FlyBase: FBti0161163
Oligonucleotides
Sequencing primers – See Table S5	Various	N/A
Software and Algorithms
Fiji	Schindelin et al., 2012	https://fiji.sc/; RRID: SCR_002285
bcl2fastq	Illumina	https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html; RRID: SCR_015058
Cell Ranger	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
scater	McCarthy et al., 2017	https://bioconductor.org/packages/release/bioc/html/scater.html; RRID: SCR_015954
Seurat	Satija et al., 2015	https://satijalab.org/seurat/; RRID: SCR_007322
SCENIC/AUCell	Aibar et al., 2017	https://aertslab.org/#scenic
NNLS Regression	Stanescu et al., 2017	N/A
Random Forest Regression – Scikit-learn	Pedregosa et al., 2011	http://scikit-learn.org/stable/; RRID: SCR_002577
Destiny	Angerer et al., 2016	http://bioconductor.org/packages/release/bioc/html/destiny.html
clusterProfiler	Yu et al., 2012	https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
GOPlot	Walter et al., 2015	http://wencke.github.io/
DESeq2	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html; RRID: SCR_015687
GOrilla	Eden et al., 2009	http://cbl-gorilla.cs.technion.ac.il/; RRID: SCR_006848
Ea-utils (fastq-mcf.)	Aronesty, 2011	https://github.com/ExpressionAnalysis/ea-utils; RRID: SCR_005553
STAR	Dobin et al., 2013	https://github.com/alexdobin/STAR; RRID: SCR_015899
pysam	Li et al., 2009	https://github.com/pysam-developers/pysam; RRID: SCR_002105
SciPy	Jones et al., 2001	https://www.scipy.org/index.html; RRID: SCR_008058
Singularity	Kurtzer et al., 2017	https://singularity.lbl.gov/index.html
Loompy	Linnarsson Lab	https://github.com/linnarsson-lab/loompy
SCopeLoomR	This Paper	https://github.com/aertslab.org/SCopeLoomR
SCopeLoomPy	This Paper	https://github.com/aertslab.org/SCopeLoomPy
SCope Source Code	This Paper	https://github.com/aertslab.org/SCope
Other
RcisTarget/SCENIC Drosophila Database	This Paper	https://aertslab.org/#scenic
SCope Resource Website	This Paper	http://scope.aertslab.org