REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-CK19	Proteintech	10712-1-AP; RRID: AB_2133325
Rabbit anti-Drebrin	Proteintech	10260-1-AP; RRID: AB_2230301
Rabbit anti-MARCKS	Proteintech	10004-2-Ig; RRID: AB_2140311
Rabbit anti-MARCKSL1	Proteintech	10002-2-AP: RRID: AB_513892
Rabbit anti-CK8	Proteintech	10384-1-AP; RRID: AB_10638912
Rabbit anti-phospho(Ser23)CK8 EP1629Y	Abcam	ab76584; RRID: AB_2049847
Goat anti-PlexinA1	R&D Systems	AF4309: RRID: AB_10645644
Mouse anti-Sema6D	SantaCruz	sc393258; RRID: AB_3099689
Rabbit anti-OCT4	Abcam	ab19657; RRID: AB_445175
AF-555 Donkey anti-rabbit IgG	Invitrogen	A31572; RRID: AB_162543
AF-633 Donkey anti-goat IgG	Invitrogen	A21082; RRID: AB_2535739
Chemicals, peptides, and recombinant proteins
RNaseZap™	Invitrogen	AM9760
M2 medium	Sigma-Aldrich	M7167
Claret FR Fluorescent Cell Linker Kit	Sigma-Aldrich	MINCLARET-1KT
TrypLE™ dissociation reagent	Invitrogen	12563011
Heat-inactivated FBS	Thermo-Fisher	10500
Donkey serum	Sigma-Aldrich	D9663
BSA	Sigma-Aldrich	A7906
DAPI	Thermo Fisher	D1306
Proteinase-K	Thermo-Fisher	EO0491
Paraformaldehyde	SantaCruz	CAS 30525-89-4
Glycerol	Fisher Scientific	G/0650/17
VectaShield	Vector Labs	H-1200
Phalloidin-Atto 550	Sigma-Aldrich	19083
Phalloidin-Atto 647N	Sigma-Aldrich	65906
HCR probe sets, amplifiers, and buffers	Molecular Instruments	HCR RNA-FISH Bundles
HBSS	Sigma-Aldrich	55037C
CMRL-1066 medium	Pan BioTech	P04-84600
KnockOut serum replacement	Gibco	10828-010
NVP-BHG712	Selleck Chemicals	A8683
Triton X-100	Sigma-Aldrich	T8787
Tween-20	Sigma-Aldrich	P1379
Deposited data
On ArrayExpress: Single-cell RNA-Seq of VE-enriched cell populations from E5.5 and E6.25 wild type mouse embryos	This paper	ArrayExpress: E-MTAB-9645
Code repository	This paper	Zenodo: 10829359
10x scRNA-Seq data	Nowotschin et al.17	https://explore.data.humancellatlas.org/projects/4e6f083b-5b9a-4393-9890-2a83da8188f1
Experimental models: Organisms/strains
Mouse: CD1	Charles River, England	Strain code: 022
Mouse: C57BL/6	In house; University of Oxford, Biomedical Services	N/A
Mouse: Hhex-GFP	Rodriguez et al.28	N/A
Mouse: Sema6D-KO	This paper: seeSTAR Methods	N/A
Oligonucleotides
Sema6d sgRNA [CUGCGAUUCGUUCGGU GAA+tracrRNA]	Sigma-Aldrich	MMPD0000123097
Sema6d F primer [5’-CAGCAGCCCAGACA TAGAGA-3’]	Invitrogen	N/A
Sema6d R primer [5’-TGCAAGCACCACAA GAGAAA-3’]	Invitrogen	N/A
Software and algorithms
Volocity, Improvisions (version: 6.3)	N/A	https://www.volocity4d.com/
Fiji ImageJ2 (version: 2.14.0/1.54f)	N/A	https://imagej.net/software/fiji/
GraphPad Prism for Windows (version: 9.5.1)	GraphPad Software Inc.	https://www.graphpad.com/features
Salmon (version: 0.13.1)	Patro et al.71	https://github.com/COMBINE-lab/salmon
STAR (version: 2.7.0f_0328)	Dobin et al.72	https://github.com/alexdobin/STAR
Velocyto (version: 0.17.17)	La Manno et al.43	https://velocyto.org/velocyto.py/
R (version: 3.5.2)	N/A	https://posit.co/download/rstudio-desktop/
Python (version: 3.9.5)	N/A	https://www.python.org/downloads/release/python-395/
Other
35 mm glass bottom dishes	MatTek Life Sciences	P35-1.5-14-C
Nunc™ Lab-Tek™ II chambered coverglass slides	Thermo Fisher	155409
8-Well μ-Slide #1.5	Ibidi	IB-80807