REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-phospho-Smad2 (IF)	Cell Signaling Technology	Cat# 8828; RRID: AB_2631089
Anti-phospho-Erk (IF and Western)	Sigma	Cat# M8159; RRID: AB_477245
Anti-Digoxigenin-AP (in situ)	Roche	Cat# 11093274910; RRID: AB_514497
Anti-Digoxigenin-HRP (in situ)	Roche	Cat# 1207733910
Anti-DNP-HRP (in situ)	Perkin Elmer	Cat# FP1129; RRID: AB_2629439
Anti-DNP-AP (in situ)	Vector Laboratories	Cat# MB-3100; RRID: AB_2336089
Anti-Rabbit Alexa Fluor 488 (IF)	Thermo Fisher Scientific	Cat# A-21206; RRID: AB_2535792
Anti-Mouse Alexa Fluor 546 (IF)	Thermo Fisher Scientific	Cat# A-10036; RRID: AB_2534012
Anti-Mouse Alexa Fluor 594 (IF)	Thermo Fisher Scientific	Cat# A-21203; RRID: AB_2535789
Anti-Rabbit Alexa Fluor 647 (IF)	Thermo Fisher Scientific	Cat# A-21244; RRID: AB_10562581
Anti-Mouse-HRP (Western)	Dako	Cat# P0447; RRID: AB_2617137
Anti-Rabbit-HRP (Western)	Dako	Cat# P0448; RRID: AB_2617138
Anti-Erk1 (Western)	Santa Cruz	Cat# sc-94; RRID: AB_2140110
Anti-Actin (Western)	Sigma	Cat# A3853; RRID: AB_262137
Anti-Smad2 (31H15L4) (ChIP)	Thermo Fisher Scientific	Cat# 700048; RRID: AB_2532277
Anti-Smad2 (D43B4) (ChIP)	Cell Signaling Technology	Cat# 5339; RRID: AB_10626777
Chemicals, Peptides, and Recombinant Proteins
SB-505124	Sigma	Cat# S4696
SU-5402	Merck	Cat# 572631
PD-0325901	Merck	Cat# 444968
NBT/BCIP tablets	Sigma	Cat# B5655
Fast Red TR/Naphthol AS-MX Tablets	Sigma	Cat# F4648
Tyramine hydrochloride	Sigma	Cat# T2879
NHS-Fluorescein ester	Thermo Fisher Scientific	Cat# 46410
Cy5 Mono NHS ester	Sigma	Cat# PA51501
Human recombinant NODAL	R&D	Cat# 3218-ND/CF
Human basic FGF	Peprotech	Cat# AF100-18b
Critical Commercial Assays
QuikChange XL Site-Directed Mutagenesis Kit	Agilent	Cat# 200516
Experimental Models: Organisms/Strains
Zebrafish Danio rerio: WT	N/A	N/A
Oligonucleotides
See Table S1 for list of all primers, cloning oligonucleotides and morpholinos	This study	N/A
Recombinant DNA
pBKS-ntl-a: probe synthesis ta: linearize Xho1: polymerase T7	Schulte-Merker et al., 1992	N/A
pAD-gal4-Lft2: probe synthesis lft2: linearize Mlu1: polymerase T7	Bisgrove et al., 1999	N/A
pBSK-flh: probe synthesis noto: linearize EcoR1: polymerase T7	Talbot et al., 1995	N/A
pBSK-fgf3: probe synthesis fgf3: linearize BamH1: polymerase T7	Kiefer et al., 1996	N/A
pBSK-fgf8a (cb110): probe synthesis fgf8a: linearize Not1: polymerase T7	https://zfin.org/ZDB-PUB-010810-1 ZFIN online publication	N/A
pBKS-sox17: probe synthesis sox17: linearize Nco1: polymerase Sp6	Alexander and Stainier, 1999	N/A
pBS-sox32 (cb527): probe synthesis sox32: linearize Not1: polymerase T7	https://zfin.org/ZDB-PUB-010810-1 ZFIN online publication	N/A
pCS2+ndr1: mRNA synthesis ndr1: linearize Not1: polymerase Sp6	Feldman et al., 1998	N/A
pCS2-dusp4: mRNA synthesis dusp4: linearize Not1: polymerase Sp6	This study	N/A
pCS2-dusp4_ATG-mut: mRNA synthesis mutant dusp4: linearize Not1: polymerase Sp6	This study	N/A
pCS2-fgf8a: mRNA synthesis fgf8a: linearize Not1: polymerase Sp6	van Boxtel et al., 2015	N/A
Software and Algorithms
FIJI (ImageJ)	Schneider et al., 2012	https://imagej.net/Fiji/Downloads
JASPAR	Mathelier et al., 2016	http://jaspar.genereg.net/