REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-CDX2	Abcam	157524; RRID:AB_2721036
Goat polyclonal anti-SOX2	R&D	AF2018; RRID:AB_355110
Goat polyclonal anti-SOX1	R&D	AF3369; RRID:AB_2239879
Rabbit polyclonal anti-SOX2	Cell Signaling	2748S; RRID:AB_823640
Rabbit polyclonal anti-PHOX2B	Jean-Francois Brunet Lab	RRID:AB_2313690
Rabbit polyclonal anti-OLIG2	Millipore	AB9610; RRID:AB_570666
Guinea pig polyclonal anti-OLIG2	Ben Novitch Lab	RRID:AB_2715520
Anti-DIG-AP antibody	Roche	11093274910; RRID:AB_514497
Mouse monoclonal anti-CDX2-PE	BD	563428; RRID: AB_2738198
Mouse monoclonal anti-SOX2-v450	BD	561610; RRID: AB_10712763
Goat polyclonal anti-SOX2	Santa Cruz	SC-17320X; RRID:AB_2286684
Chemicals, Peptides, and Recombinant Proteins
bFGF	R&D	3139-FB
CHIR99021	Axon	1386
Critical Commercial Assays
Nextera DNA library prep kit	Illumina	FC-121-1030
Kapa Hyper Prep Kit	Illumina	KK8502
In-Fusion Cloning Kit	Takara	639650
Phusion High-Fidelity PCR Master Mix	ThermoFisher Scientific	F532L
Deposited Data
ATAC-seq on ESCs undergoing directed differentiation toward defined neural fates	This paper	ArrayExpress accession E-MTAB-6337
Sox2 ChIP-seq in hindbrain and spinal cord neural progenitors differentiated from mouse embryonic stem cells	This paper	ArrayExpress accession E-MTAB-6348
Experimental Models: Cell Lines
HM1 mESCs	Thermo Scientific, MES4303	Doetschman et al., 1987
T/Bra−/− mESCs	James Briscoe Lab	Gouti et al., 2017
Cdx1,2,4−/− mESCs	James Briscoe Lab	Gouti et al., 2017
iCDX2 ESCs	Hitoshi Niwa (provided by Myriam Hemberger, Babraham Institute)	5ECER4G20; Niwa et al., 2005
Experimental Models: Organisms/Strains
Mouse: Sox2eGFP	Robin Lovell-Badge Lab	MGI:3589809, Ellis et al., 2004
Mouse: TCF/Lef:H2B-mCherry	This paper	N/A
Chicken: Dekalb strain	Henry Stewart & Co.	N/A
Oligonucleotides
Primers for RT-qPCR	This paper	Table S5
Primer: mCherry forward: ATGGTGAGCA AGGGCGAG	This paper	N/A
Primer: mCherry reverse: CTTGTACAGC TCGTCCATGC	This paper	N/A
Primers for indexing ATAC-seq libraries	Buenrostro et al., 2013	Table S6
Primer: TCF/Lef:H2B:mCherry cloning forward: GGGCTCTAGGGATCCATCGATGGGAACA AAAGCTGGTACCGG	This paper	N/A
Primer: TCF/Lef:H2B:mCherry cloning reverse: GGTACCCGGGGATCCATCGATCGCTTACA ATTTACGCCTTAAGATACATTGATGAG	This paper	N/A
Recombinant DNA
Chicken Cdx2 RNA in situ hybridization probe	Source Bioscience	EST Clone ChEST626o23
pJC5-4	Chung et al., 1993	N/A
Tcf./Lef:H2B-GFP	Addgene	32610
Software and Algorithms
All data analysis scripts used in this paper	This paper	https://github.com/luslab/NeuralATACseq
Fiji	Schindelin et al., 2012	http://fiji.sc/
GraphPad Prism 7	GraphPad	https://www.graphpad.com/
Trim Galore! v0.4.1	N/A	https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
Bowtie2 v2.3.2	Langmead and Salzberg, 2012	https://sourceforge.net/projects/bowtie-bio/files/bowtie2/
Piccard v2.9.2	N/A	https://broadinstitute.github.io/picard/
DeepTools v3.0.0	Ramírez et al., 2016	https://deeptools.readthedocs.io/en/develop/
MACS2 v2.1.0	Zhang et al., 2008	https://github.com/taoliu/MACS/
IDR framework	Li et al., 2011	https://sites.google.com/site/anshulkundaje/projects/idr/deprecated
BEDTools v2.26.0	Quinlan and Hall, 2010	https://bedtools.readthedocs.io/en/latest/
Subread v1.5.0	Liao et al., 2013	http://subread.sourceforge.net/
GREAT v3.0.0	McLean et al., 2010	http://great.stanford.edu/public/html/index.php
HOMER v4.9.1	Heinz et al., 2010	http://homer.ucsd.edu/homer/motif/
i-cisTarget 2015	Imrichová et al., 2015	https://gbiomed.kuleuven.be/apps/lcb/i-cisTarget/
R v3.4.0	R Foundation	https://www.r-project.org/
DESeq2 v1.18.1	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
SOM v0.3-5.1	N/A	https://cran.r-project.org/web/packages/som/som.pdf
CENTIPEDE v1.2	Pique-Regi et al., 2011	http://centipede.uchicago.edu/
GenomicRanges v1.30.3	Lawrence et al., 2013	https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html
LOLA v1.8.0	Sheffield and Bock, 2016	http://bioconductor.org/packages/release/bioc/html/LOLA.html
Motifmatchr v1.0.1	N/A	https://github.com/GreenleafLab/motifmatchr
ChIPseeker v1.14.2	Yu et al., 2015	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
Limma v3.34.3	Ritchie et al., 2015	https://bioconductor.org/packages/release/bioc/html/limma.html
Oligo v1.42.0	Carvalho and Irizarry, 2010	https://bioconductor.org/packages/release/bioc/html/oligo.html
Other
ENCODE data portal	ENCODE Project Consortium, 2012, Sloan et al., 2016	https://www.encodeproject.org/
JASPAR database	Khan et al., 2018	http://jaspar.genereg.net/
4DGenome database	Teng et al., 2015	https://4dgenome.research.chop.edu/
GENCODE release M14	Mudge and Harrow, 2015	https://www.gencodegenes.org/mouse_releases/14.html