KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Bacterial and Virus Strains
Biological Samples
Chemicals, Peptides, and Recombinant Proteins
PFA	Sigma-Aldrich	Cat#158127, Cat#P6148
Hydrogen peroxide (H2O2)	Sigma-Aldrich	Cat#H1009
KOH	Sigma-Aldrich	Cat#P5958
Formamide, deionized	Amresco	Cat#4170848
Proteinase K	Sigma-Aldrich	Cat#3115836001
30% sucrose	Sigma-Aldrich	Cat#84100
O.C.T.	Sakura	Cat#4583
poly-lysine	Sigma-Aldrich	Cat#P8920
Atto 647N NHS ester	Millipore Sigma	Cat#18373
Atto 550 NHS ester	Millipore Sigma	Cat#92835
Papain Dissociation System	Worthington	Cat#LK003150
Torula RNA	Sigma-Aldrich	Cat#83850
20X SSC	Invitrogen/Ambion	Cat#AM9770
EnGen Cas9 NLS, S. pyogenes	NEB	Cat#M0646
Critical Commercial Assays
10X Reagents	10X Genomics	Chromium Single Cell 3′v2 Reagent Kits
EnGen sgRNA Synthesis Kit, S. pyogenes	NEB	Cat#E3322
Deposited Data
Raw data files for scRNA-Seq	NCBI GEO	TBD
Experimental Models: Cell Lines
Experimental Models: Organisms/Strains
Zebrafish scGESTALT.2	This paper	N/A
Oligonucleotides
Recombinant DNA
pT2Olactb:loxP-dsR2-loxP-EGFP	gift from Atsushi Kawakami (Yoshinari et al., 2012)	N/A
Software and Algorithms
Cell Ranger	10X Genomics	https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/installation
URD	Farrell et al., 2018	https://github.com/farrellja/URD
NMF modules	Farrell et al., 2018	https://github.com/YiqunW/NMF
Seurat v2.3.4	Butler et al., 2018	https://satijalab.org/seurat/
R, RStudio	RStudio	https://rstudio.com
Other
scRNA-seq resource	This paper	https://github.com/brlauuu/zf_brain
scGESTALT lineage resource	This paper	https://scgestalt.mckennalab.org/