REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Tyrosine hydroxylase	Millipore	RRID: AB_90755
Beta-III tubulin (TUJ1)	Covance	RRID: AB_2313773
HDAC4	Abcam	RRID: AB_298903
β-actin	Abcam	RRID: AB_2305186
PDI	Cell signaling	RRID: AB_2156433
FKBP9	Abcam	RRID: AB_10562617
Ero1-Lα	Cell signaling	RRID: AB_823683
TSPAN7	Novus biologicals	RRID: AB_11035060
Na+/K+-ATPaseα3 (ATP1A3)	Santa cruz	RRID: AB_10848453
Rtn1/2	Santa cruz	RRID: AB_2183564
PRKCB	ProSci	Cat#43-319
LAMP1	Santa cruz	RRID: AB_626853
LC3B	Sigma	RRID: AB_796155
TRA-1-60	Biolegend	RRID: AB_1186144
Nanog	Cell signaling	RRID: AB_10694485
Biological Samples
OX1-19/SFC841-03-1/2	EBiSC	UOXFi004-B/ STBCi044-B
JR053-1/6	EBiSC	UOXFi005-A/ UOXFi005-B
AH016-3/6	EBiSC	University of Oxford
SFC156-03-01	EBiSC	STBCi101-A
SFC840-03-06	EBiSC	STBCi026-D
SFC067-03-01	EBiSC	STBCi105-A
MK088-1	EBiSC	UOXFi003-A
RH058-03	EBiSC	STBCi025-A/B/C
MK082-26	EBiSC	UOXFi002-A
MK071-3	EBiSC	UOXFi001-B
SFC077-03-04	EBiSC	STBCi268-A
SFC844-03-12	EBiSC	STBCi294-A
SFC120-03-04	EBiSC	STBCi043-B
SFC865-03-07	EBiSC	STBCi298-A
Chemicals, Peptides, and Recombinant Proteins
ROCK inhibitor (Y27632 dihydrochloride)	Bio-Techne	Cat#1254
Tasquinimod	Tocris	Cat#S7617
Okadaic acid	Abcam	Cat#O7885
LB100	Tocris	Cat#S7537
Cantharidin	Tocris	Cat#1548
LDN-193189	Sigma	Cat#SML0559
SB-431542	Bio-Techne	Cat#1614
SHH C24II	Bio-Techne	Cat#1845-SH-500
Purmorphamine	Bio-Techne	Cat#4551/10
FGF8a	Stratech	Cat#16124-HNAE-SIB
CHIR-99021	Bio-Techne	Cat#4423
BDNF	Peprotech	Cat#450-02
GDNF	Peprotech	Cat#450-10
TGFb3	Peprotech	Cat#100-36E
DAPT	Abcam	Cat#ab120633
Ascorbic acid	Sigma	Cat#A4544
(db)-cAMP	Sigma	Cat#D0627
hESC-qualified Matrigel	Corning	Cat#354277
DQ BSA Red	Thermo Fisher Scientific	Cat#D12051
NucBlue Live ReadyProbes	Thermo Fisher Scientific	Cat#R37605
Critical Commercial Assays
Cytotune v1 Sendai Reprogramming kit	Thermo Fisher Scientific	A13780-01
Cytotune v2 Sendai Reprogramming kit	Thermo Fisher Scientific	A16517
β-Actin qPCR Control Kit	Eurogentec	SR-CL004-005
Human-HT-12-v4 expression BeadChip Kit	BD	BD-103-0204
All-Prep DNA/RNA Mini kit	QIAGEN	80204
RNeasy FFPE kit	QIAGEN	Cat#73504
RNA 6000 pico kit	Agilent	Cat#5067-1513
Quant-iT RiboGreen RNA kit	Thermo Fisher Scientific	Cat#R11490
Nextera XT DNA Library Prep Kit	Illumina	Cat#FC-131-1096
RNeasy Micro kit	QIAGEN	Cat#74004
Superscript III reverse transcriptase kit	Thermo Fisher Scientific	Cat#18080093
Fast SYBR green master mix	Thermo Fisher Scientific	Cat#4385612
αSyn extracellular release MSD kit	Meso Scale Discovery	Cat#K151TGD-2
Deposited Data
Raw RNA-seq data	ArrayExpress	ArrayExpress: E-MTAB-7303
Software and Algorithms
Harmony	Perkin Elmer	N/A
GenomeStudio	Illumina	N/A
Karyostudio	Illumina	N/A
TrimGalore v0.4.1	(Krueger, 2015)	https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Kallisto v0.42.5	(Bray et al., 2016)	https://pachterlab.github.io/kallisto/
Picard 2.0.1	(Picard Toolkit, 2018)	https://broadinstitute.github.io/picard/
HISAT2	(Kim et al., 2015)	https://ccb.jhu.edu/software/hisat2/index.shtml
Tximport 1.4.0	(Soneson et al., 2015).	https://bioconductor.org/packages/release/bioc/html/tximport.html
Scater 1.8.0	(McCarthy et al., 2017)	https://bioconductor.org/packages/release/bioc/html/scater.html
Cellity 1.8.0	(Ilicic et al., 2016)	https://bioconductor.org/packages/release/bioc/html/cellity.html
DESeq2	(Love et al., 2014),	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
goseq	(Young et al., 2010)	https://bioconductor.org/packages/release/bioc/html/goseq.html
The R project for statistical computing	R Development Core Team, 2008	https://www.r-project.org/
switchde 1.6.0	(Campbell and Yau, 2017)	https://bioconductor.org/packages/release/bioc/html/switchde.html
Ouija 0.99.0	(Campbell and Yau, 2017)	https://github.com/kieranrcampbell/ouija/
scran 1.8.2	(Lun et al., 2016)	https://bioconductor.org/packages/release/bioc/html/scran.html
Phenotypic Linkage Network	(Honti et al., 2014).	https://github.com/csandorfr/AP-PLN