REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rat monoclonal anti-CTIP2	Abcam	Cat #ab18465
Mouse monoclonal anti-S100β	Abcam	Cat #ab11178
Rabbit polyclonal anti-TBR1	Abcam	Cat #ab31940
Rat monoclonal anti-pH3	Abcam	Cat #ab10543
Mouse monoclonal anti-NEUN	Millipore	Cat #MAB377
Mouse monoclonal anti-VGLUT2	Millipore	Cat #MAB5504
Chicken polyclonal anti-TBR2	Millipore	Cat #AB15894
Mouse monoclonal anti-NESTIN	Millipore	Cat #MAB353
Mouse monoclonal anti-SATB2	SCBT	Cat #sc-81376
Rabbit polyclonal anti-CUX1	SCBT	Cat #sc-13024
Mouse monoclonal anti-RORβ	R&D Systems	Cat #PP-H3925-00
Chicken polyclonal anti-GFP	Aves labs	Cat #GFP-1020
Rabbit polyclonal anti-pH3	Sigma-Aldrich	Cat #H0412
Mouse monoclonal anti-KI67	BD Pharmingen	Cat #550609
Rat monoclonal anti-KI67	Affymetrix	Cat #14-5698
Rabbit polyclonal anti-PAX6	BioLegend	Cat #901301
Mouse monoclonal anti-PAX6	DSHB	Cat #AB_528427
Rabbit polyclonal anti-RFP	MBL	Cat #PM005
Rabbit polyclonal anti-BRN2	GeneTex	Cat #GTX114650
Rabbit polyclonal anti-PDZRN3 Novus	Biologicals	Cat #NBP2-55802
Rabbit polyclonal anti-PTX3	Barbara Bottazzi Humanitas research, Italy	N/A
Rabbit polyclonal anti-PRDM16	Patrick Seale UPenn, U.S.A.	N/A
Rabbit polyclonal anti-H3K27ac	abcam	Cat #ab4729
Rabbit polyclonal anti-H3K4me	abcam	Cat #ab8895
Goat polyclonal anti-Mouse Alexa Fluor 488	Thermo Fisher	Cat #A11001
Goat polyclonal anti-Mouse Alexa Fluor 546	Thermo Fisher	Cat #A11003
Goat polyclonal anti-Mouse Alexa Fluor 647	Thermo Fisher	Cat #A21235
Goat polyclonal anti-Chicken Alexa Fluor 488	Thermo Fisher	Cat #A11039
Goat polyclonal anti-Rabbit Alexa Fluor 488	Thermo Fisher	Cat #A11034
Goat polyclonal anti-Rabbit Alexa Fluor 546	Thermo Fisher	Cat #A11010
Goat polyclonal anti-Rabbit Alexa Fluor 647	Thermo Fisher	Cat #A21244
Goat polyclonal anti-Rat Alexa Fluor 488	Thermo Fisher	Cat #A11006
Bacterial and Virus Strains
Replication-incompetent enhanced GFP-expressing retrovirus	(Palmer et al., 1999)	N/A
Chemicals, Peptides, and Recombinant Proteins
EGS [ethylene glycolbis(succinimidylsuccinate)]	Thermo Scientific	Cat #21565
Blocking reagent for nucleic acid hybridization	Roche	Cat #11096176001
Critical Commercial Assays
Ovation Ultralow System V2 1–16	NuGEN	Cat #0344
Ovation RNA-Seq System V2	NuGEN	Cat #7102
RecoverAll Total Nucleic Acid Isolation	Ambion	Cat #AM1975
Click-iT EdU Imaging	Invitrogen	Cat #C10340
Deposited Data
RNA-seq data	This paper	GEO: GSE111660
ChIP-seq data	This paper	GEO: GSE111657 GSE111658, GSE11 1659, GSE111661
Experimental Models: Cell Lines
HEK-293 retrovirus packaging cell line	(Palmer et al., 1999)	293gp NIT-GFP
Experimental Models: Organisms/Strains
Mouse: C57BL/6	Charles River laboratories	Strain code: 027
Mouse: CD-1	Charles River laboratories	Strain code: 022
Mouse: B6.129-Prdm16tm1.1Brsp/J	The Jackson laboratory	Stock #024992
Mouse: Emx1tm1(cre)Krj/J	The Jackson laboratory	Stock #005628
Mouse: B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J	The Jackson laboratory	Stock #007914
Mouse: Neurod6tm1(cre)Kan	(Goebbels et al., 2006)	MGI: 5308766
Oligonucleotides
Primers: in situ hybridization, exon 4–8 probe. Forward: 5′-CTGGCTCAAGTACATCCGTGT-3′ Reverse: 5′-CGTGCTGTGGATATGCTTGT-3′	(Bjork et al., 2010a)	N/A
Primers: in situ hybridization, exon 9 probe. Forward: 5′-CTGTACCCACGACCACCTCT-3′ Reverse: 5′-GACTTTGGCTCAGCCTTGAC-3′	This paper	N/A
Primers: Prdm16 shRNA, exon 5. Forward: 5′-GTTGGTGCATGTGAAAGAATTCAAGAGATTCTTTCACATGCACCAAC-3′ Reverse: 5′-GTTGGTGCATGTGAAAGAATCTCTTGAATTCTTTCACATGCACCAAC-3′ Primers: scrambled control. Forward: 5′-GCGGAGAAAGTGGATTTATTTCAAGAGAATAAATCCACTTTCTCCGC-3′ Reverse: 5′-GCGGAGAAAGTGGATTTATTCTCTTGAAATAAATCCACTTTCTCCGC-3′	(Bjork et al., 2010b)	N/A
Primers: Pdzrn3 shRNA, exon 10. Forward: 5′-GCTCAGAACAGGAGAATAACGTTCAAGAGACGTTATTCTCCTGTTCTGAGCCTTTTTG-3′ Reverse: 5′-AATTCAAAAAGGCTCAGAACAGGAGAATAACGTCTCTTGAACGTTATTCTCCTGTTCTGAGC-3′ Primers: scrambled control. Forward: 5′-GCAAGGACAGACACGGAATATTTCAAGAGAATATTCCGTGTCTGTCCTTGCCTTTTTG-3′ Reverse: 5′-AATTCAAAAAGGCAAGGACAGACACGGAATATTCTCTTGAAATATTCCGTGTCTGTCCTTGC-3′	(Honda et al., 2010)	N/A
Primers: PR domain deletion. Forward: 5′-GAAGGTGCCTACTCCTTG-3′ Reverse: 5′-TGGGATTGGAATGTCTTC-3′	This paper	N/A
Primers: Real-time PCR analysis Prdm16, exons 9 and10. Forward: 5′-TGCTAAGCCTTCACCGTTCT-3′ Reverse: 5′-TCTTTCAGGACTCCCACAGG-3′ Gabra2, exons 5 and 6. Forward: 5′-ATGCCCACTGAAATTTGGAA-3′ Reverse: 5′-AGCAACCTGAACGGAGTCAG-3′ Diras2, single exon. Forward: 5′-CAGGAACTCCTCAACCTGGA-3′ Reverse: 5′-CCCTTGAGCTTCTCCTTCCT-3′ Pdzrn3, exons 5 and 6. Forward: 5′-GAGAAGAGCTGGAGCTGGAA-3′ Reverse: 5′-TCCCAATGTCATCTTCGTCA-3′ Sema6d, exons 13 and 14. Forward: 5′-CCTTCTCTAGCTGCGTGGTC-3′ Reverse: 5′-ACCAACCACAGTACGGGTCA-3′ Ptx3, exons 1 and 2. Forward: 5′-TGGACAACGAAATAGACAATGG-3′ Reverse: 5′-TCTCCAGCATGATGAACAGC-3′ Tmem35, exons 1 and 2. Forward: 5′-CAGCAAGGATGCCTACAGTG-3′ Reverse: 5′-GATGGAATTGATGCCCATTT-3′ Kremen1, exons 2 and 3. Forward: 5′-GCGAGCACAATTATTGCAGA-3′ Reverse: 5′-GCAGGCAGGAATTTCACAGT-3′ Itga6, exons 20 and 21. Forward: 5′-CCAAAGGTTTGGAGCAGATT-3′ Reverse: 5′-TTTCAGGAAGTTCCCGTTTC-3′ Adamts20, exons 6–9. Forward: 5′-GTCAGAATGTCCCGGATGAT-3′ Reverse: 5′-AAGCCTAACGTGTCGCATTT-3′ Lifr, exons 10–12. Forward: 5′-ACCACAGAAGCCACTCCTTC-3′ Reverse: 5′-GGTAAAGGCTTCCAGTAGACGA-3′ Epha3, exons 8 and 9. Forward: 5′-TCCTCACGGTGGTCACCTAT-3′ Reverse: 5′-TTAAGTGGCCATTCCCAAAG-3′ Lama1, exons 14 and 15. Forward: 5′-TTCTGCTAAAATGGCGCTCT-3′ Reverse: 5′-GGGACATTCACAGTGTTCCA-3′ Veph1, exons 10 and 11. Forward: 5′-TTGAAGTCGCCATGACAGAG-3′ Reverse: 5′-TTTCACTGAAGCCAAACACG-3′ Slc14a2, exons 8 and 9. Forward: 5′-CTGTGCATACATGGGAGCTG-3′ Reverse: 5′-GGTGAGGGTGGAGAGACAGA-3′ Smoc1, exons 5 and 6. Forward: 5′-TTGAGCCAGGGTAATTCAGG-3′ Reverse: 5′-ACACAGGTTGGGTCTCCATC-3′ Palmd, exons 3 and 4. Forward: 5′-CAAAATCAGCAAGACCAGCA-3′ Reverse: 5′-TTTGCAGTTCAGCCTTTTCA-3′ Eva1c, exons 5–7. Forward: 5′-TACGCATGTGTTCCCAAGAA-3′ Reverse: 5′-CCGCTTGGGTTGAATGTTAT-3′	This paper	N/A
Dscaml1, exons 12 and 13. Forward: 5′-AATGGCGATGAAGTGGTCTC-3′ Reverse: 5′-ATCAAACCTCGGTCCTCTCC-3′ Tox1, exons 1–3. Forward: 5′-TGCCTGGACCCCTACTATTG-3′ Reverse: 5′-CTTGGTCCAGGGTAGGACTG-3′ Thsd4, exons 4 and 5. Forward: 5′-GGCCTATCGGCAGTACAAAC-3′ Reverse: 5′-CCATGAATGGCTTGTTGTTG-3′ Adamts18, exons 6 and 7. Forward: 5′-CAAAGATGGGACCATTGGAA-3′ Reverse: 5′-TGGTCTGCATGGTGATTGAT-3′ Meis1, exons 9 and 10. Forward: 5′-AAAAAGCAGTTGGCACAAGA-3′ Reverse: 5′-GGTCTATCATGGGCTGCACT-3′	This paper	N/A
Fluorescent in situ hybridization
RNAscope probe Mm Pdzrn3	Advanced Cell Diagnostics	Cat #517061
RNAscope probe Mm Itga6	Advanced Cell Diagnostics	Cat #441701
RNAscope probe Mm Gabra2	Advanced Cell Diagnostics	Cat #435011
RNAscope probe Mm Tubb3	Advanced Cell Diagnostics	Cat #423391
Recombinant DNA
pCAG-TAG	Addgene	Plasmid #26771
CAG-GFP-IRES-CRE	Addgene	Plasmid #48201
pCAGIG	Addgene	Plasmid #11159
pCMV-VSV-G	Addgene	Plasmid #8454
Hes5-Luc	Addgene	Plasmid #41724
pcDNA3.1 Prdm16	Addgene	Plasmid #15503
pCAG-Prdm16-IRES-GFP	This paper	N/A
Hes5p-Prdm16-IRES-GFP	This paper	N/A
Hes5p-ΔPRdm16-IRES-GFP	This paper	N/A
pCAGIG Pdzrn3	This paper	N/A
Software and Algorithms
ImageJ/ Fiji 1.49S	Wayne Rasband National Institutes of Health, U.S.A.	https://imagej.nih.gov/ij/
Imaris 7.0	Bitplane	http://www.bitplane.com/releasenotes/imaris700.aspx
Integrative Genomics Viewer (IGV) 2.3	Broad Institute MIT/Harvard	http://software.broadinstitute.org/software/igv/
MATLAB R2017b	MathWorks	https://www.mathworks.com/products/matlab.html
Cutadapt	(Martin, 2011)	http://code.google.com/p/cutadapt/
STAR	(Dobin et al., 2013)	http://code.google.com/p/rna-star/
FeatureCounts	(Liao et al., 2014)	http://subread.sourceforge.net
DESeq2	(Love et al., 2014)	http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html
gProfiler	(Reimand et al., 2007)	http://biit.cs.ut.ee/gprofiler/
REVIGO	(Supek et al., 2011)	http://revigo.irb.hr/
Bowtie2 2.2.8	(Langmead et al., 2009)	http://bowtie.cbcb.umd.edu
MACS2 2.1.1	(Zhang et al., 2008)	https://pypi.python.org/pypi/MACS2
IDR R package	(Li et al., 2011)	http://cran.rproject.org/web/packages/idr/index.html
HOMER v4.6 suite	(Heinz et al., 2010)	http://homer.ucsd.edu/homer/
DeepTools2	(Ramírez et al., 2016)	deeptools.iefreiburg.mpg.de
BETA v1.0.7	(Wang et al., 2013)	http://cistrome.org/BETA/