REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
H3K27ac antibody	Abcam	Cat#Ab4729; RRID: AB_2118291
IgG antibody	Millipore	Cat#12-370; RRID: AB_145841
Critical Commercial Assays
RNAqueous Micro Total RNA isolation kit	Ambion	Cat#AM1931
SmartSeq2 V4 kit	Takara Clontech	Cat#634889
Nextera XT library preparation kit	Illumina	Cat#FC-131-1024
Dynabeads Protein A	Life Technologies	Cat#10006D
Dynabeads Streptavidin M-280	Invitrogen	Cat#11206D
MicropPlex Library Preparation kit	Diagenode	Cat#05010012
NextSeq ® 500/550 High Output Kit v2 (75 cycles)	Illumina	Cat#FC-404-2005
Nextera DNA kit	Illumina	Cat#FC-121-1030
NEB Next High-Fidelity 2X PCR Mas-ter Mix	New England Biolabs	Cat#M0543S
Long Range HotStart PCR kit	KAPA Biosystems	Cat#KK3501
InFusion HD Cloning kit	Clontech	Cat#638910
DIG RNA Labelling Kit	Roche	Cat#11277073910
Deposited Data
RNA-seq data (inc. single cell)	This paper	ShinyApp GEO: GSE106676, Pagoda https://github.com/tsslab/foxd3
ChIP-seq data	This paper	ShinyApp GEO: GSE106676
ATAC-seq data	This paper	ShinyApp GEO: GSE106676
Experimental Models: Organisms/Strains
Zebrafish Gt(foxd3-citrine)ct110	Sauka-Spengler laboratory	ct110
Zebrafish Gt(foxd3-mCherry)ct110R	Sauka-Spengler laboratory	ct110R
TgBAC(foxd3-Avi-2A-Citrine)ox161	Sauka-Spengler laboratory	ox161
Tg(ubiq:NLS-BirA-2A-Cherry)ox114	Sauka-Spengler laboratory	ox114
Recombinant DNA
BAC clone CH211-196F13	CHORI https://bacpacresources.org	CH211-196F13
Software and Algorithms
Sickle	Joshi and Fass (2011)	https://github.com/najoshi/sickle
STAR 2.4.2a	Dobin et al. (2013)	https://github.com/alexdobin/STAR
FeatureCounts (v1.4.6-p4)	Liao et al. (2014)	http://bioinf.wehi.edu.au/featureCounts
R v3.4.2	R Core Team	https://www.r-project.org/
DESeq2 (v.1.14.1)	Love et al. (2014)	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
edgeR	Robinson et al. (2010)	https://bioconductor.org/biocLite.R
SCDE	Fan et al. (2016)	http://hms-dbmi.github.io/scde/index.html
PAGODA	Fan et al. (2016)	http://hms-dbmi.github.io/scde/index.html
Bowtie (v.1.0.0)	Langmead et al. (2009)	http://bowtie-bio.sourceforge.net/bowtie2/index.html
Bedtools (v.2.15.0)	Langmead et al. (2009)	https://github.com/arq5x/bedtools
MACS2 (v2.1.0)	Zhang et al. (2008)	https://github.com/taoliu/MACS
HOMER (v.4.4)	Heinz et al. (2010)	http://homer.ucsd.edu/homer/index.html
SeqMINER	Ye et al. (2011)	http://seqminer.genomic.codes
Deeptools (v.2.2.2)	Ramírez et al. (2016)	https://github.com/deeptools/deepTools
MEME suite	Bailey et al. (2015)	http://meme-suite.org/doc/download.html
Gimmemotifs (v.0.9.0.3)	van Heeringen and Veenstra (2011)	https://gimmemotifs.readthedocs.io/en/master/
GREAT	McLean et al. (2010)	http://great.stanford.edu/public/html/
DiffBind	Stark and Brown (2011)	https://bioconductor.org/packages/release/bioc/html/DiffBind.html