class_name	class_category	description	aliases_or_subclasses	derived_from	derived_from_explanation
CGE_NR2F2/PROX1	initial	Newborn neurons from the caudal ganglionic eminence			
LGE-OB_MEIS2/PAX6	initial	Newborn neurons of the LGE_MEIS2/PAX6 class which are found in the adult olfactory bulb	GC-2 (doi: 10.1016/j.celrep.2018.11.034)		
LGE_FOXP1/ISL1	initial	Newborn neurons of the inner LGE which are FOXP1/ISL1 positive			
LGE_FOXP1/ISL1/NPY1R	initial	A ventral subclass of LGE_FOXP1/ISL1, which is EBF1 negative and NPY1R positive, and is apparently distinct early in differentiation			
LGE_FOXP1/PENK	initial	Newborn neurons of the inner LGE which are FOXP1/PENK positive			
LGE_FOXP2/TSHZ1	initial	Newborn neurons from the external/dorsal LGE which are FOXP2/TSHZ1 positive and FOXP1/NPY negative. We observe in immunos and transcriptome trajectories they are likely SP8 and SCGN positive until they become strongly FOXP2 positive, at which point those genes become undetectable.			
LGE_MEIS2/PAX6	initial	Newborn neurons of the external/dorsal LGE which are MEIS2/PAX6/TSHZ1/SCGN(macaque only)/ETV1/FOXP2(but barely detectable with immunofluorescence) positive and FOXP1/NR2F2 negative			
LGE_MEIS2/PAX6/SCGN	initial	A subclass of LGE_MEIS2/PAX6 which is also positive for CALB2, ZIC1 and SCGN in the mouse, and is apparently distinct early in differention.			
MGE_CRABP1/MAF	initial	Newborn neurons of the MGE which are CRABP1/MAF/NKX2-1/ETV1/LHX6 positive and are seen migrating through the MGE and striatum by RNAscope.			
MGE_CRABP1/TAC3	initial	A sister initial class to MGE_CRABP1/MAF. Appears by RNAscope to become LHX8+/- only after reaching striatal destinations. Adult terminal classes covered by Krienen et al. (doi: 10.1038/s41586-020-2781-z)			
MGE_LHX6/MAF	initial	Newborn neurons from the MGE which are positive for NKX-1/LHX6/MAF/MAFB/ERBB4/SST			
MGE_LHX6/NPY	initial	Newborn neurons from the MGE which may be postmitotic derivatives from MGE_LHX6/MAF, but appear to distribute to the basal nuclei as well as the cortex. Expresses LHX6/MAF/NPY/CORT/CHODL. See Ctx/BN_SST/CHODL.			
RMTW_ZIC1/RELN	initial	Newborn Cajal-Retzius neurons found in cortical layer 1 and derived from the Rostro-medial telencephalic wall (RMTW). Highly expresses RELN. Appear to be glutamatergic, but express low levels of GAD genes. Reported to mostly disappear before maturity, and no corresponding terminal class is observed in adult.	Cajal-Retzius Cells, Horizontal Cells of Cajal		
VMF_CRABP1/LHX8	initial	These cells may arise from the MGE-like GBX1+ portion of the septum.			
VMF_LHX1/POU6F2	initial	POH or POA-derived neurons expressing PAX6/NR2F2/ISL1/SP8/MEIS2/LHX1/TSHZ2, reported to become TH+/SCGN+/- hypothalamic dopaminergic cells	may contribute to dopaminergic groups A11-15 (doi: 10.1038/s41467-020-18231-z / doi:10.1016/j.tins.2007.03.006)		
VMF_NR2F2/LHX6	initial	Neurons with a VMF expression profile that are NR2F2/LHX6/CALB1 positive. Found in mouse MGE, CGE and cortex dissections with unknown derivative adult profile. This is a possible source of POA derived cortical interneurons (doi: 10.7554/eLife.32017 , doi: 10.1523/JNEUROSCI.4068-11.2011)			
VMF_PEG10/DLK1	initial	POH or POA-derived newborn neurons that express PEG10/DLK1/HMX3/HAP1/TSHZ2/NR2F2. These cells are reported to cross the telencephalon-diencephalon boundary and to populate the amygdala. (doi: 10.1038/nn.2556)			
VMF_TMEM163/OTP	initial	Hypothalamus-derived newborn neurons that express VMF_TMEM163/OTP. These cells appear to be excitatory, their top marker is SLC17A6. Thus they are not included in our taxonomy, nor does their derivative terminal class(es) appear to make thresholds to be included in the dataset.			
VMF_ZIC1/ZIC2	initial	Septum-derived newborn neurons expressing ZIC1/2/3/4. Adult septum is undersampled in both macaque and mouse, and so derivative terminal class may be missing from dataset.			
Amy/Hypo_HAP1/PEG10	terminal	These cells were found in both hypothalamus and amygdala mouse samples. They appear to be the neurons which are reported to cross the telencephalon-diencephalon boundary and to populate the amygdala (doi: 10.1038/nn.2556). Interestingly their expression suggests they use both GABA and Glutamate neurotransmitters.		VMF_PEG10/DLK1 or VMF_TMEM163/OTP	
BN-eSPN_FOXP2/TSHZ1	terminal	This terminal class appears to consist of two related classes which coclustered in our leiden clustering. In the striatum cells express CASZ1/OTOF and are known as eccentric spiny neurons (eSPNs). The other clear subclass is derived from amygdala samples, where these cells are known as intercalated cells (ITCs). In both locations they express FOXP2/4 but do not express FOXP1	eccentric spiny neurons, intercalated cells of the amygdala, D1H(doi:10.1016/j.neuron.2019.11.004), PCDH8+ SPNs(doi:10.1016/j.celrep.2016.06.059)	LGE_FOXP2/TSHZ1 	We believe the preponderance of the evidence points to LGE_FOXP2/TSHZ1 being the precursor of BN-eSPN_FOXP2/TSHZ1. This is supported by the RNA velocity absorption analysis, the more perfect matching of markers like OPRM1, CASZ1 and lack of FOXP1 in macaque and mouse, expression of CASZ1 in the dorsal/external LGE where SCGN/FOXP2 are also seen (histology), trajectory expression showing that immature cells of FOXP2/TSHZ1 expressing SCGN, SP8 and ETV1. LGE_FOXP1/ISL1 is also a possible source but we believe the partial transcriptomic correspondence between LGE_FOXP1/ISL1 and BN-eSPN_FOXP2/TSHZ1 is spuriously driven by activation of shared projection markers and DRD1 as these neurons mature.
Ctx/BN_SST/CHODL	terminal	This terminal class is distributed to the cortex and also the basal nuclei. In the cortex these neurons are well known for high expression of SST and CHODL. They also likely correspond to hippocampal SST/NPY/NOS1+ ivy and neurogliaform (NGF) cells (doi:10.1523/JNEUROSCI.5123-09.2010 ). 	cortical long-projecting SST+ neurons, hippocampal ivy and NGF cells, striatal plateau low-threshold-spiking neurons	MGE_LHX6/NPY	
Ctx_CCK/DPY19L1	terminal	Rare class of cortical interneurons		CGE_NR2F2/PROX1	
Ctx_CCK/VIP	terminal	Common CCK+ VIP+/- class of CGE-derived cortical interneurons	CCK basket cells, VIP bipolar cells	CGE_NR2F2/PROX1	
Ctx_LAMP5/NDNF	terminal	Class of cortical/hippocampal formation interneurons	Adarb2/Ndnf-HPF cells in Allen taxonomy.	CGE_NR2F2/PROX1	
Ctx_LHX6/LAMP5	terminal	LHX6/LAMP5+ class of cortical chandelier interneurons	CHC2 Cortical Chandelier Cells (doi:10.1038/s41586-018-0654-5)	MGE_LHX6/MAF	This class is reported to be derived from NKX2-1+ cells using Cre-Lox lineage tracing(doi:10.1016/j.cell.2017.08.032, Paul et al). We find that the most parsimonious explanation is that these are MGE derived interneurons which bear transcriptomic similarity to CGE-derived LAMP5 cells due to very high expression of LAMP5.
Ctx_LHX6/PVALB	terminal	Common PVALB+ MGE-derived cortical interneurons	PVALB basket cells, fast spiking interneurons	MGE_LHX6/MAF	
Ctx_LHX6/SST	terminal	Common SST+ MGE-derived cortical interneurons	Martinotti SST+ interneurons	MGE_LHX6/MAF	
Ctx_NR2F2/PAX6	terminal	Rare class of cortical interneurons.	Adarb2/Pax6 cells in Allen taxonomy.	CGE_NR2F2/PROX1 or VMF classes or (unlikely) LGE_MEIS2/PAX6	Terminal class doesn't express MEIS2/FOXP2/STXBP6/ETV1 or any other markers which would be expected from LGE derived cells but expresses CGE/VMF marker NR2F2, and RNA velocity suggests CGE_NR2F2/PROX1 is more likely as origin.
Ctx_PROX1/LAMP5	terminal	Common LAMP5+ class of CGE-derived cortical interneurons	Lamp5 interneurons	CGE_NR2F2/PROX1	
Ctx_PROX1/SNCG	terminal	Common SNCG+ class of CGE-derived cortical interneurons	Sncg interneurons	CGE_NR2F2/PROX1	
Ctx_PVALB/VIPR2	terminal	PVALB/VIPR2+ class of cortical chandelier interneurons.	CHC1 Cortical Chandelier Cells (doi:10.1038/s41586-018-0654-5)	MGE_CRABP1/MAF or MGE_LHX6/MAF	RNA velocity analysis is unclear as to which MGE class is the more likely precursor initial class. Cortical PVALB cells are assumed to descend from MGE_LHX6/MAF class, while striatal PVALB cells descend from MGE_CRABP1/MAF, (doi: 10.1016/j.celrep.2018.07.053), but the Ctx_PVALB/VIPR2 class is distinct from the Ctx_LHX6/PVALB class and shows transcriptional similarities to both candidate initial classes, for instance sharing PTHLH and continuing adult NKX2-1 expression with MGE_CRABP1/MAF.
Ctx_SST/NDNF	terminal	SST/NDNF+ class of cortical interneurons		MGE_LHX6/MAF	
GP_GBX1/GABRA1	terminal	GBX1/GABRA1/PVALB/ZIC1 neurons which appear to make up a large percentage of the neurons in the globus pallidus	fast-spiking “prototypical” globus pallidus neurons (doi: 10.1016/j.cell.2018.07.028)	VMF_CRABP1/LHX8	
OB-GC NR2F2/PENK	terminal	A class of granule cells of the olfactory bulb	GC-6 (doi: 10.1016/j.celrep.2018.11.034)	LGE_MEIS2/PAX6 (LGE-OB_MEIS2/PAX6) 	
OB-GC_RPRM	terminal	A rare class of granule cells of the olfactory bulb	GC-3 (doi: 10.1016/j.celrep.2018.11.034)	LGE_MEIS2/PAX6 or LGE_FOXP2/TSHZ1	
OB-GC_STXBP6/PENK	terminal	The most prominent class of granule cells of the olfactory bulb	GC-5 (doi: 10.1016/j.celrep.2018.11.034)	LGE_MEIS2/PAX6 (LGE-OB_MEIS2/PAX6)	
OB-PGC_FOXP2/CALB1	terminal	FOXP2/CALB1 positive periglomerular cells (PGC) of the olfactory bulb	PGC-3 (doi: 10.1016/j.celrep.2018.11.034), calbindin+ PGC	LGE_FOXP2/TSHZ1	
OB-PGC_TH/SCGN	terminal	MEIS2/PAX6/ETV1/TH/SCGN positive periglomerular cells of the olfactory bulb and accessory olfactory bulb	PGC-2 (doi: 10.1016/j.celrep.2018.11.034), dopaminergic group A16 (doi: 10.1016/S0165-0173(00)00034-5 / doi.org/10.1016/j.tins.2007.03.006 short axon dopaminergic cells, THLI striatum cells	LGE_MEIS2/PAX6/SCGN or LGE_MEIS2/PAX6	We believe that TH/SCGN+ PSCs are derived from this group rather than the hypothalamic VMF_LHX1/POU6F2 as PSCs are negative for NR2F2, in addition to their location far removed from the telencephalon-diencephalon boundary.
OB-PGC_ZIC	terminal	CALB2/SP8/ETV1/ZIC1/2/4 positive periglomerular cells of the olfactory bulb	PGC-1 (doi: 10.1016/j.celrep.2018.11.034)	LGE_MEIS2/PAX6 or septum	
Str-IN_CRABP1/MAF	terminal	Striatal GABAergic interneurons CRABP1/ETV1/NKX2-1/KIT/MAF+ in adult rodent and primates.	TH+ (MGE-derived) striatal interneurons, PVALB+ (MGE-derived) striatal interneurons, PTHLH+ (MGE-derived) striatal interneurons	MGE_CRABP1/MAF	
Str-IN_CRABP1/TAC3	terminal	Striatal GABAergic interneurons CRABP1/ETV1/NKX2-1/MAF/TAC3/STXBP6+ in adult primates but not rodents, nor laurasiatherians.	TAC3+ (MGE-derived) striatal interneurons	MGE_CRABP1/TAC3	
Str-dSPN_FOXP1/ISL1	terminal	Direct (striatonigral projecting) spiny projection neurons (DRD1+) of the basal nuclei. Subclasses include orthogonal axes of variation which appear to be overlaid later in development such as dorsoventral and patch-matrix gene expression identities, perhaps due to striosome cells appearing to be born before matrix cells in mouse (doi:10.1016/j.neuron.2018.06.021.)	dSPN, direct medium spiny neuron	LGE_FOXP1/ISL1	
Str-iSPN_FOXP1/PENK	terminal	Indirect (striatopallidal projecting) spiny projection neurons (DRD2+) of the basal nuclei. Subclasses include orthogonal axes of variation which appear to be overlaid later in development such as dorsoventral and patch-matrix gene expression identities.	iSPN, indirect medium spiny neuron	LGE_FOXP1/PENK	
Str_LHX8/CHAT	terminal	Cholinergic cells of the basal nuclei and septum which express ZIC1/CHAT/LHX8 and choline transporters	cholinergic striatal interneurons, septohippocampal cholinergic pathway cells	VMF_CRABP1/LHX8	
DWMIN_NR2F2/SP8	terminal	The terminal class identity and transcriptome is unknown. We observed many cells matching these markers in the deep white matter at late developmental and mature ages in the macaque, but can't speculate about them beyond noting their existence in large numbers.		CGE_NR2F2/PROX1 (Presumed), VMF also possible	Presumed to be CGE derived, but could also be POA/POH derived given the small number of markers observed in immunostaining
DWMIN_MEIS2/PAX6	terminal	The terminal class full transcriptome is unknown. Deep white matter inhibitory neurons (DWMIN) derived from the arc and arc-ACC migratory streams. They appear to express MEIS2/PAX6/SP8/SCGN and low/no FOXP2, TH or NR2F2 protein.	Possible component of Allen cortical Meis2	LGE_MEIS2/PAX6	While it was unclear whether mature cortical DWMIN_MEIS2/PAX6 cells in the adult mouse clustered with olfactory bulb or were hidden amongst another larger terminal class, Figure 4 and ED provides evidence that neurons of class migrate into and remain in the deep white matter.
SWMIN_FOXP2/FOXP4	terminal	The terminal class full transcriptome is unknown. Superficial white matter inhibitory neurons (SWMIN), which appear to derive from a medial migratory stream from the LMS which continues into VMPFC. Their existence is largely based upon LGE_FOXP2/TSHZ1 cells found in cortical developing macaque samples, and FOXP2/SP8 or FOXP2/DLX2 stains in macaque superficial white matter. These cells appeared very rare in histology.	Likely component of Allen cortical Meis2	LGE_FOXP2/TSHZ1	Macaque transcriptome and histology suggests these cells still express some SP8 and SCGN while migrating. These cells did not cluster distinctly in mouse adult data.
Str-SLN_TH/SCGN	terminal	The terminal class full transcriptome is unknown. These striatum laureatum neurons wreaTHe the boundaries of the striatum (especially externally), including the claustrum. These cells share many markers with OB-PGC_TH/SCGN, however this requires further transcriptomic characterization. These cells express MEIS2/PAX6/SP8/TH/SCGN but do not appear to express FOXP2 (SPN), NKX2-1 (MGE-derived striatal interneuron) or NR2F2 (CGE or POA/POH-derived). It appears that most studies of TH+ cells of the striatum don't distinguish between Str-SLN_TH/SCGN and Str-IN_CRABP1/MAF/TH. Informally called wreaTH cells.		LGE_MEIS2/PAX6/SCGN or LGE_MEIS2/PAX6 (presumed)	
G1-phase_SLC1A3/ATP1A1	technical	Cells in G1-phase of cell cycle			
S-phase_MCM4/H43C	technical	Cells in S-phase of cell cycle			
G2-M_UBE2C/ASPM	technical	Cells in G2/M phase of cell cycle			
Transition	technical	Cells of multiple classes which aren't well distinguished by leiden clustering due to cell cycle and early maturation variation. Excluded from most analyses to avoid cross contamination of initial classes			
Glia	technical	Diverse glial cells which pass filters to be part of the dataset but are not analyzed here.			
Excitatory	technical	Excitatory cells which pass filters to be part of the dataset. Expresses SLC17A6/7 and tiny amount of GAD or DLX genes, so are not analyzed