REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
mouse anti-SMI32	Covance	# SMI-32P; RRID:AB_2314912
mouse anti-TuJ1	Sigma	MAB1637; RRID:AB_2210524
rabbit anti-GFAP	Dako	Z0334; RRID:AB_10013382
mouse anti-Map2a/b	Sigma	M1406; RRID:AB_477171
rabbit anti-nestin	Millipore	ABD69; RRID:AB_2744681
Goat anti-human Islet-1	R&D	AF1837; RRID:AB_2126324
Rat anti-Nkx-6.1	DSHB	F55A10-s; RRID:AB_532378
Chemicals, peptides, and recombinant proteins
Hoechst 33258	Sigma	33258
IMDM	Life Technologies	12440061
F12	Life Technologies	11765062
NEAA	Life Technologies	11140-50
B27	Life Technologies	17504044
N2	Life Technologies	17502048
Anti/Anti	Life Technologies	15240062
LDN193189	Cayman Chemical	19396
CHIR99021	Xcess bioscience	M60002
SB431542	Cayman Chemical	13031
All-trans RA	Stemgent	04-0021
SAG	Cayman Chemical	11914
Rock Inhibitor (Y-27632)	Stemcell Technologies	72308
db-cAMP	Millipore	28745
Compound E	Calbiochem	565790
DAPT	Cayman Chemical	13197
Ascorbic Acid	Sigma-Aldrich	A4403
BDNF (-80)	Peprotech	450-02
GDNF (-80)	Peprotech	450-10
Critical commercial assays
QIAamp DNA Blood mini Kit	Qiagen	51104
Qiagen RNeasy mini kit	Qiagen	74104
Ribo-Zero Gold rRNA depletion and Truseq Stranded total RNA kit	Illumina	20020598
Biognosys iRT mixture	Biognosys	Ki-3002-2
Expedeon FASP protocol	Abcam	ab270519
BCA assay	Pierce	23227
Nextera XT DNA Library Preparation Kit	Illumina	FC-131-1096
Deposited data
ATAC-seq	This paper	http://lincsportal.ccs.miami.edu/dcic-portal/
RNA-Seq	This paper	http://lincsportal.ccs.miami.edu/dcic-portal/
Proteomics	This paper	https://chorusproject.org/pages/dashboard.html#/search/Neurolinc/projects
Whole-Genome Sequencing	This paper	http://data.answerals.org/search#root-neurolincs
Experimental models: Cell lines
Control human iPSC 25iCTR	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS25iCTR-18nxx
Control human iPSC 83iCTR	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS83iCTR-33nxx
Control human iPSC 00iCTR	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS00iCTR-nxx
ALS human iPSC 29iALS	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS29iALS-C9nxx
ALS human iPSC 52iALS	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS52iALS-C9nxx
ALS human iPSC 30iALS	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS30iALS-C9nxx
ALS human iPSC 28iALS	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS28iALS-C9nxx
Control human iPSC 002iCTR	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS0002iCTR-nxx
Control human iPSC 0179iCTR	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS0179iCTR-nxx
Control human iPSC 0201iCTR	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS0201iCTR-nxx
Control human iPSC 0206iCTR	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS0206iCTR-nxx
Control human iPSC 1ATZiCTR	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS1ATZiCTR-nxx
Control human iPSC 1WP3iCTR	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS1WP3iCTR-nxx
Control human iPSC 9XH7iCTR	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS9XH7iCTR-nxx
ALS human iPSC 0BUUiALS	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS0BUUiALS-nxx
ALS human iPSC 2YNLiALS	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS2YNLiALS-nxx
ALS human iPSC 6UC9iALS	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS6UC9iALS-nxx
ALS human iPSC 6ZLDiALS	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS6ZLDiALS-nxx
ALS human iPSC 7VCZiALS	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS7VCZiALS-nxx
ALS human iPSC 9YHNiALS	The Cedars-Sinai Biomanufacturing Center (iPSC Core)	CS9YHNiALS-nxx
Experimental models: Organisms/strains
D. melanogaster: knocking-down or overexpressing these genes downstream of UAS sites for GAL4-specific modulation	Bloomington Drosophila Stock Center
Software and algorithms
Burrows-Wheeler Aligner BWA-MEMv0.7.8	Li and Durbin, 2009	http://bio-bwa.sourceforge.net/
Picard tools (v1.83)	http://broadinstitute.github.io/picard/	http://picard.sourceforge.net
Genome Analysis Toolkit (GATK v3.4.0)	DePristo et al., 2010; McKenna et al., 2010	https://gatk.broadinstitute.org/hc/en-us
HTSeq	Anders et al. (2015)	https://htseq.readthedocs.io/en/master/overview.html
DESeq2	Love et al. (2014)	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Ingenuity pathway analysis	https://www.qiagenbioinformatics.com/products/ingenuitypathway-analysis	https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/
Gorilla	Eden et al. (2009)	http://cbl-gorilla.cs.technion.ac.il/
Cytoscape	Otasek et al., 2019	https://cytoscape.org/
edgeR	Robinson et al., 2010	https://bioconductor.org/packages/release/bioc/html/edgeR.html
OpenSWATH	http://openswath.org/en/latest/index.html	http://openswath.org/en/latest/
HOMER	Heinz et al. (2010)	http://homer.ucsd.edu/homer/motif/
MACS2	Zhang et al. (2008)
Image-Pro Insight v9	https://www.mediacy.com/support/imageproinsight	https://www.mediacy.com/support/imageproinsight
ProteoWizard v.3.0.6002	Kessner et al., 2008	https://sourceforge.net/p/proteowizard/mailman/proteowizard-support/?viewmonth=201407
Trans Proteome Pipeline v.4.8	Keller et al., 2005	http://tools.proteomecenter.org/software.php
OmicsIntegrator2 package (v2.3.1)	Tuncbag et al. (2016)	https://github.com/fraenkel-lab/OmicsIntegrator2/