REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-βIII Tubulin	SIGMA-Aldrich	Cat#T2200, RRID:AB_262133
Rat anti-Ctip2	Abcam	Cat#ab123449; RRID: AB_10973033
Mouse anti-Pvim	Abcam	Cat#ab20346; RRID: AB_445527
Rabbit-Satb2	Abcam	Cat#ab92446; RRID: AB_10563678
Anti-goat Alexa 594	Jackson ImmunoResearch	Cat#705-585-003; RRID: AB_2340432
Anti-human IgG	Jackson ImmunoResearch	Cat# 111-225-144, RRID:AB_2338021
Cy2 AffiniPure Goat Anti-Rabbit IgG (H + L)	Jackson ImmunoResearch	Cat# 111-225-144, RRID:AB_2338021
Goat anti-Human IgG (H + L), Alexa Fluor 594 Conjugated	Thermo Fisher Scientific	Cat#A11014 RRID:AB_1500628
Rabbit Anti-Green Fluorescent Protein (GFP) Polyclonal Antibody	Thermo Fisher Scientific	Cat# A-11122; RRID: AB_221569
Donkey anti-Rabbit IgG (H + L) Secondary Antibody, Alexa Fluor 488	Thermo Fisher Scientific	Cat # A21206; RRID: AB_2535792
Mouse Mitochondria alpha antibody	Millipore	MAB1273; RRID: AB_94052
Mouse HNK1 IgM antibody	Hybridoma Bank	Cat # 3H5; RRID: AB_2314644
Anti-mouse IgM Secondary Antibody, Alexa Fluor 647	Thermo Fisher Scientific	Cat# A21238 RRID: AB_2535807
Anti-mouse IgG, Secondary antibody, Alexa Fluor 555	Thermo Fisher Scientific	Cat # A32773 RRID: AB_2762848
Anti-HA	SIGMA-Aldrich	Cat#H3663; RRID: AB_262051
Anti-FLAG	SIGMA-Aldrich	Cat#F1804; RRID: AB_262044
Anti-6xHis Tag	Thermo Fisher Scientific	Cat#372900; RRID: AB_2533309
Anti-Penta-His antibody	QIAGEN	Cat#34660; RRID: AB_2619735
Anti-mouse Alexa 488	Abcam	Cat#ab150117; RRID: AB_2688012
Anti-rabbit Alexa 647	Abcam	Cat#ab150083; RRID: AB_2714032
Anti-mouse Cy5 secondary antibody	Abcam	Cat#ab97037; RRID: AB_10681024
Anti-rabbit Alexa 488	Abcam	Cat#ab150077; RRID: AB_150077
Anti-Mouse Cy3 secondary antibody	Abcam	Cat#ab97035; RRID: AB_10680176
Anti-Human IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 568	Thermo Fisher Scientific	Cat# A-21090, RRID:AB_2535746
Anti-Actin antibody	Abcam	Cat# ab179467; RRID:AB_2737344
Placental alkaline phosphatase monoclonal antibody (8B6.18)	Thermo Fisher Scientific	Cat # MA5-12694; RRID: AB_10978663
Mouse anti-human IgG1-HRP	Serotec	Cat # MCA514P
Chemicals, peptides, and recombinant proteins
Neurobasal medium	Invitrogen	Cat#A3582901
Penicillin Streptomycin	GIBCO	Cat#155140148
L-Glutamine	Life Technologies	Cat#25030-024
MEM Non-Essential Amino Acids solution	Life Technologies	Cat#11140035
B27 Supplement	GIBCO	Cat#17504044
Dako Mounting medium	Agilent	Cat#S3023
Fast green FCF stain	SIGMA-Aldrich	Cat#2353-45-9
Triton X-100	CarlRoth	Cat#3051
High Capacity Streptavidin Agarose beads	Thermo Fisher Scientific	Cat#20357
Streptavidin, Alexa Fluor 594 conjugate	Thermo Fisher Scientific	Cat#S11227
Probe- Mm-Unc5d-C2 RNAscope	Advanced Cell Diagnostics	Cat#480461-C2
Probe- Mm-Gpc3 - c1 RNAscope	Advanced Cell Diagnostics	Cat#418541
Dulbecco’s Modified Eagle Medium (DMEM) GlutaMAX	Thermo Fisher Scientific	Cat#31966-021
Fetal Bovine Serum (FBS)	SIGMA-Aldrich	Cat#F7524
Amphotericin B	SIGMA-Aldrich	Cat#A2942
Paraformaldehyde 32%	Electron microscopy science	Cat#15714-S
Triton 100X	Sigma-Aldrich	Cat#T9284
BSA - BSA	Sigma-Aldrich	Cat#A7906
Hoechst	Thermo Fisher Scientific	Cat# H21486
JetPrime reagent	PolyPlus - Ozyme	Cat#Pol114-15
Phosphate buffered saline, pH 7.4	Life Technologies	Cat#10010023
HEPES Free Acid 1M Solution	SIGMA-Aldrich	Cat#7365-45-9
DMEM, high glucose, pyruvate, no glutamine-500 mL	Life Technologies	Cat#21969035
IPTG	SIGMA-ALDRICH	Cat#I6758-1G
Terrific Broth	Fisher Scientific	Cat#12891660
Fetal Bovine Serum (FBS)	GIBCO	Cat#10437028
Dapi Staining Solution	Abcam	Cat#ab228549
High Capacity Streptavidin Agarose Resin	Thermo Fisher Scientific	Cat#10733315
Magnesium Sulfate, Anhydrous	SIGMA-Aldrich	Cat#746452-500G
Ampicillin Sodium Salt Biochemica	AppliChem	Cat#A0839.0025
Streptavidin from Streptomyces Avidinii	SIGMA-Aldrich	Cat#S4762-5MG
Paraformaldehyde, Powder 95%	SIGMA-Aldrich	Cat#158127-100G
Immu-mount	Thermo Fisher Scientific	Cat#10622689
Polyethylenimine (PEI)	SIGMA-Aldrich	Cat#208727
Sucrose	SIGMA-Aldrich	Cat#S0389-500G
Human IgG, Fc fragment	Jackson Immunoresearch	Cat#009-000-008-JIR
NDSB-256	Hampton Research	Cat#HR2-705
RPMI-1640 Medium	LGC Standards	Cat#ATCC 30-2001
1-Step Ultra TMB-ELISA HRP	Thermo Fisher Scientific	Cat # 34,028
Sodium deoxycholate (NaDOC)	SIGMA-Aldrich	Cat #30970
NP-40	SIGMA-Aldrich	Cat #18896
Sodium Chloride (NaCl powder)	SIGMA-Aldrich	Cat #S3014
Tris hydrochloride (Tris-HCl powder)	SIGMA-Aldrich	Cat #10812846001
Complete Protease Inhibitor Cocktail	Roche Diagnostics	Cat #04693116001
Critical commercial assays
RNAscope Universal Pretreatment Kit	Advanced Cell Diagnostics	Cat#322380
RNAscope Fluorescent Multiplex Reagent Kit	Advanced Cell Diagnostics	Cat#320850
Bio-Rad protein assay	Biorad	Cat#5000001
Nucleospin RNAII kit	Macherey-Nagel	Cat#740955-10
iScript cDNA Synthesis Kit	BioRad	Cat#1708890
LightCycler480 SYBRGreen I Master1 kit	Roche Life Science	Cat#04707516001
Neon Transfection System 100 μL Kit	Thermo Fisher Scientific	Cat#MPK10025
Deposited data
Mouse single-cell RNAseq data	di Bella et al. (2021)	Cat#GSE153164
Human and mouse RNAseq data (aRG, bRG and migrating neurons)	Florio et al. (2015)	Cat#GSE65000
Human Neuroblastoma tumor single-cell RNAseq data	Dong et al. (2020)	Cat#GSE137804
PDB	This study	7ZAV1
PDB	This study	7ZA2
PDB	This study	7ZA3
PDB	This study	7ZAV
PDB	This study	7ZAW
Experimental models: Cell lines
Primary cortical neurons and cortex tissue from	Charles River (Maintained at the Animal Facility of Faculty of Medicine (University of Barcelona)	C57BL/6 background
SY5Y	ATCC	ATCC® CRL-2266™
IGR-N91	Laboratory of J. Bénard, Gustave Roussy Institute, Villejuif, France	Described in Ferrandis and Bénard, 1993
SHEP	Laboratory of M. Schwab, Institute for Experimental Pathology, Heidelberg, Germany.	Described in Ciccarone et al., (1989))
IMR32	ATCC	ATCC® CCL-127™
HEK293T	ATCC	CRL-3216; RRID: CVCL_0063
HEK293S	ATCC	CRL-3022; RRID: CVCL_A785
K562	ATCC	CCL-243; RRID: CVCL_0004
N2A	ATCC	ATCC® CCL-131™
WK6	ATCC	ATCC® 47,078™
C3A	ATCC	ATCC® CRL-10741™
Experimental models: Organisms/strains
Embryonated eggs, naked neck strain	Elevage avicole du Grand Buisson, Saint Maurice sur Dargoire, France	N/A
Oligonucleotides
ISH: GPC3-foward GCCGAAGAAGGGAACTGATTC	This study	N/A
siRNA Universal Negative Control #1	SIGMA-Aldrich	SIC001
human GPC3 siRNA; NM_004484	SIGMA-Aldrich	SASI_Hs01_00205845
PrimerPCR SYBR Green Assay: UNC5A, Human UniqueAssayID: qHsaCID0013056	Biorad	10,025,636
PrimerPCR SYBR Green Assay: UNC5B, Human UniqueAssayID: qHsaCID0021074	Biorad	10,025,636
PrimerPCR SYBR Green Assay: UNC5C, Human UniqueAssayID: qHsaCID0016268	Biorad	10,025,636
PrimerPCR SYBR Green Assay: UNC5D, Human UniqueAssayID: qHsaCED0045738	Biorad	10,025,636
PrimerPCR SYBR Green Assay: GPC3, Human UniqueAssayID: qHsaCID0016381	Biorad	10,025,636
shRNA for GPC3 knockdown: GCCGAAGAAGGGAACTGATTC	This study	N/A
Primer: Nanoglue and Nanobreak in pCAGIG and pHLSec Forward: GTAGCTGAAACCGGTCAGGTGCAGCTG GTCGAGTCTGGGG	This study	N/A
Primer: Nanoglue and Nanobreak in pCAGIG Reverse: AATTTACGTAGC GGCCGCCTAAGACAGATCCT CTTCTGAGATG	This study	N/A
Primer: Nanoglue and Nanobreak in pHLSec Reverse: GGAACCTC CGGTACCTTGGCCTCCCGGG CCGGCCGCTGGTTG	This study	N/A
Primer: hGPC3, hGPC3UG, hGPC3core, hGPC3coreUG Forward: TCTCAGG CCGAATTCATGGCCGGGACC GTGCGCACCGCGTG	This study	N/A
Primer: hGPC3 and hGPC3UG Reverse: GTGGTGCTTGGTACCTCAGTGCACCA GGAAGAAGAAGCACACC	This study	N/A
Primer: hGPC3core and hGPC3coreUG Reverse: GGAACCTCCGGTACC AACTCTACCTTTGGGCATAGACATGG	This study	N/A
Primer: hGPC3UG and hGPC3coreUG (N241Q) Forward: ggaattgaagtgatc CaGacaactgatcacctgaagttcagtaag	This study	N/A
Primer: hGPC3UG and hGPC3coreUG (N241Q) Reverse: gatcacttcaattccaagattcagag	This study	N/A
Primer: mGPC3ecto, mGPC3 488 and mGPC3core Forward: GTAGCTGAAACCG GTgacgccacctgtcaccaggtccgttc	This study	N/A
Primer: mGPC3ecto Reverse: GTGGTGCTTGGTACCggacg gcatgttccccacgctgtg	This study	N/A
Primer: mGCP3 488 Reverse: GTGGTGCTTGGTACCatc caggcttttatccagaac	This study	N/A
Primer: mGCP3core Reverse: GTGGTGCTTGGTACCtttacc cttgggcacagacatggttc	This study	N/A
Primer: mUnc5Aecto Forward: TCTC AGGCCGAATTCGCCACCATGGCTG TGCGACCTGGACTGTGGCCTGC	This study	N/A
Primer: mUnc5Aecto Reverse: GGAACCTCCGGTACCCACGTC CTCAGGGCCAGAGCTGGTGTG	This study	N/A
Primer: mUnc5AectoGU Forward: AGCTGCACCAACCCTAATCCCACC AATGGCGGCGCTTTCTGCGAG	This study	N/A
Primer: mUnc5AectoGU Reverse: AGGGTTGGTGCAGCTTCTGC TTCTCTTCTG	This study	N/A
Primer: mUnc5Becto Forward: GTAGCTGAAACCGGTtaccc atacgatgttccagattacg	This study	N/A
Primer: mUnc5Becto Reverse: GGAACCTCCGGTACCatctc ccgatgtctccagggtcagcac	This study	N/A
Primer: mUnc5BectoGU Forward: ACCTGCACCAACCCAAATCCAAC CAATGGTGGGGCCTTCTGTGAG	This study	N/A
Primer: mUnc5BectoGU Reverse: TGGGTTGGTGCAGGTTCT TGTGCGTTTCTG	This study	N/A
Recombinant DNA
Plasmid: pCAGIG	Matsuda and Cepko, 2004	Cat#11159 (Addgene)
Plasmid: pCAG-miR30	Matsuda and Cepko, 2007	Cat#14758 (Addgene)
Plasmid: BLBP-GFP	Shariati et al. (2013)	Cat#63174 (Addgene
Plasmid: pCAGGS-mCherry	Gurtan et al., 2012	Cat#41583 (Addgene)
Plasmid: pHLSec	Addgene	Cat#99845
Plasmid: pADL-23c	Antibody Design Labs	SKU: PD0111
Software and algorithms
Prism, version 8	Graphpad Software, USA	https://www.graphpad.com/
ImageJ (Fiji), version 1.53f51	Schneider et al., 2012	https://doi.org/10.1038/nmeth.2089
ImageJ (Fiji), version 1.53f51	Schindelin et al., 2012	https://doi.org/10.1038/nmeth.2019
CellProfiler, version 2.2.0	CellProfiler, USA	https://cellprofiler.org
RStudio, version 1.4.1106	RStudio, USA	https://www.rstudio.com/
DEP-LFQ package for R, BiocManager 1.30.16	CRAN repositories	https://bioconductor.org/packages/devel/bioc/vignettes/DEP/inst/doc/DEP.html
Seurat package for R, version 4.0.2	Satija Lab	https://satijalab.org/seurat/
Prism 9.0	GraphPad Software, USA	RRID:SCR_002798
DIALS (via XIA2)	Winter et al., 2013, 2018	https://doi.org/10.1107/S0907444913015308 https://doi.org/10.1107/S2059798317017235
CCP4 package	Winn et al., 2011	https://doi.org/10.1107/S0907444910045749
Staraniso		https://staraniso.globalphasing.org/cgi-bin/staraniso.cgic
Phenix	Liebschner et al., 2019	https://doi.org/10.1107/S2059798319011471
COOT	Emsley and Cowtan, 2004	https://doi.org/10.1107/S0907444904019158
REFMAC	Murshudov et al., 2011	https://doi.org/10.1107/S0907444911001314
CCP4i2 interface	Potterton et al., 2018	https://doi.org/10.1107/S2059798317016035
Super-Pose	Maiti et al., 2004	https://doi.org/10.1093/nar/gkh477
Privateer, MKIV version	Agirre et al., 2015	https://doi.org/10.1038/nsmb.3115.
AceDRG	Long et al., 2017	https://doi.org/10.1107/S2059798317000067
MODELLER	Webb and Sali, 2016	https://doi.org/10.1002/cpbi.3
GROMACS 2020	Abraham et al., 2015	https://doi.org/10.1016/j.softx.2015.06.001
AMBER14SB force field	Maier et al., 2015	https://doi.org/10.1021/acs.jctc.5b00255
MDAnalysis	Michaud-Agrawal et al., 2011	https://doi.org/10.1002/jcc.21787
Alpha Fold	Jumper et al., 2021; Varadi et al., 2022	https://doi.org/10.1038/s41586-021-03819-2 https://doi.org/10.1093/nar/gkab1061
VMD	Humphrey et al., 1996	https://doi.org/10.1016/0263-7855(9600018-5)
Multi-Seq VMD plugin	Roberts et al. (2006)	https://doi.org/10.1186/1471-2105-7-382
CHARMM-GUI glycan modeler	Park et al. (2019)	https://doi.org/10.1093/glycob/cwz003
BI-Aevaluation	Biacore, Cytiva	https://www.cytivalifesciences.com
Xcalibur 4.1	Thermo Fisher Scientific	https://www.thermofisher.com
MaxQuant software (Version 1.6.3.4)	Cox and Mann (2008); Cox et al. (2011)	https://doi.org/10.1093/glycob/cwz003 https://doi.org/10.1021/pr101065j
Other
Series S Sensor Chip CM5	Cytiva	Cat#29149603