Transcriptomic and spatial organization of telencephalic GABAergic neurons

Abstract

The telencephalon of the mammalian brain contains multiple regions and circuits that have adaptive and integrative roles in a variety of brain functions. GABAergic neurons in the telencephalon are diverse; they have many circuit functions, and dysfunction of these neurons has been implicated in various brain disorders^1-3. Here we conducted a systematic and in-depth analysis of the transcriptomic and spatial organization of GABAergic neuronal types in all regions of the mouse telencephalon and their developmental origins. This was accomplished using 611,423 young adult single-cell transcriptomes and 614,569 single-cell transcriptomes collected from multiple prenatal and postnatal developmental timepoints. We present a hierarchically organized adult telencephalic GABAergic neuronal cell-type taxonomy of 7 classes, 52 subclasses, 284 supertypes and 1,051 clusters, as well as a corresponding developmental taxonomy of 1,688 clusters across ages from embryonic day 7 to postnatal day 14. Detailed charting efforts reveal extraordinary complexity whereby relationships among cell types reflect both spatial locations and developmental origins. Transcriptomically and developmentally related cell types are often found in distant and diverse brain regions, indicating that long-distance migration and dispersion is a common characteristic of nearly all classes of telencephalic GABAergic neurons. Moreover, we find various spatial dimensions of both discrete and continuous variation among related cell types that are correlated with gene expression gradients. Lastly, we find that cortical, striatal and some pallidal GABAergic neurons undergo extensive postnatal diversification, whereas septal, preoptic and most pallidal GABAergic neuronal types emerge in a burst during the embryonic stage with limited postnatal diversification. Overall, the telencephalic GABAergic cell-type taxonomy will serve as a foundational reference for molecular, structural and functional studies of cell types and circuits by the entire community.

Fig. 1. Transcriptomic taxonomy of telencephalic GABAergic neuronal types in mice.

a, The transcriptomic taxonomy of 284 supertypes organized in a dendrogram (10xv2, n = 269,307 cells; 10xv3, n = 342,116 cells). At each class or subclass branch, the top marker genes are shown. From the top down, the bar plots represent major neurotransmitter (NT) type and region distribution of profiled cells. NA, not applicable. b–d, UMAP representation of all cell types coloured by subclass (b), supertype (c) and the dissection region (d). e, Representative MERFISH sections of the adult mouse brain across forebrain structures coloured by cell class. Each class is labelled by its ID and shown in the same colour as in the dendrogram in a. The triangular schematic denotes the hierarchical level shown in the panel. C, class. All class, subclass and region abbreviations are listed in Supplementary Table 1.

Fig. 2. MGE-derived GABAergic neuronal types in the CTX and CNU.

a–c, UMAP representation of all MGE cells coloured by subclass (a), supertype (b) or the broad brain region (c). d, Constellation plot of MGE clusters using UMAP coordinates shown in b. The nodes are clusters coloured by supertype (ST) and grouped in bubbles by subclass. The lines around the subclass bubbles denote the two classes—CTX–MGE GABA and CNU–MGE GABA. e–m, Representative MERFISH sections showing the location of supertypes in MGE subclasses 50 (Lamp5 Lhx6 Gaba) (e), 51 (Pvalb chandelier Gaba) (f), 52 (Pvalb Gaba) (g), 53 (Sst Gaba) (b), 54 (STR Prox1 Lhx6 Gaba) (i), 55 (STRv Lhx8 Gaba) (j), 56 (Sst Chodl Gaba) (k), 57 (NDB–SI–MA–STRv Lhx8 Gaba) (l) and 58 PAL–STR Gaba–Chol (m). Cells are coloured and labelled by supertype. The triangular schematic denotes the most granular hierarchical level shown in the panels. All class, subclass and region abbreviations are listed in Supplementary Table 1.

Fig. 3. LGE-derived GABAergic neuronal types of the CNU.

a, Constellation plot of LGE clusters using UMAP coordinates shown in b. Nodes are labelled by cluster ID, coloured by supertype and grouped in bubbles by subclass. b, UMAP representation of all LGE cells coloured by supertype. c–g, Representative MERFISH sections showing the location of LGE subclasses 59 (GPe Sox6 Cyp26b1 Gaba) (c), 63 (STR D1 Sema5a Gaba) (d), 64 (STR–PAL Chst9 Gaba) (e), 60 (OT D3 Folh1 Gaba) (f) and 65 (IA Mgp Gaba) (g). Cells are coloured and labelled by supertype. h,i, Representative MERFISH sections showing the location of CNU–LGE subclasses 61 (STR D1 Gaba) (h) and 62 (STR D1 Gaba) (i). Each box contains one supertype and cells are labelled and coloured by cluster to highlight the diversity. The triangular schematics denote the most granular hierarchical level shown in c–g (supertype) and h and i (cluster (CL)). BLA, basolateral amygdalar nucleus; BMA, basomedial amygdalar nucleus; CLA, claustrum. All class, subclass and region abbreviations are listed in Supplementary Table 1.

Fig. 4. Organization of GABAergic neuronal types across the sAMY and BST.

a, Representative MERFISH sections showing the locations of subclasses belonging to the CNU–HYa GABA class. Cells are coloured and labelled by subclass (SC). A, anterior; P, posterior. b,c, Representative MERFISH sections showing the locations of cells belonging to the MEA–BST subclasses (b) and CEA–BST subclasses (c). Each row shows one subclass, and cells are coloured and labelled by supertype. Within each subclass, each supertype’s locations in both the MEA and BST (b) or both the CEA and BST (c) are shown, indicating the existence of the same cell type in these locations. d–f, Spatial domain clustering within BST neurons using BANKSY. The alluvial plot (d) shows the relationship between subclasses present in the BST and the spatial domains. Spatial domains corresponding to subclasses that are shared with MEA or CEA are labelled as MEA domains or CEA domains, respectively. Representative MERFISH images show the location of the spatial domains, with cells coloured by spatial domain identity (e) and the area covered by each domain (f). Triangular schematics denote the most granular hierarchical level shown in the panels. All class, subclass and region abbreviations are listed in Supplementary Table 1.

Fig. 5. TFs and developmental trajectories of telencephalic GABAergic neurons.

a, Expression of key TFs in each supertype in the adult subpallium GABAergic neuron taxonomy tree. Genes labelled in red have exemplary developmental in situ hybridization (ISH) images shown in Extended Data Fig. 15b. b–e, UMAP representation of all cell types across the developmental time course from E7 to P56, coloured by age (b), class (c), adult subclass (d) and major developmental lineage gene markers (e). In this global UMAP, only the 10xv3 cells are included for the P56 timepoint. All class, subclass and region abbreviations are listed in Supplementary Table 1.

Fig. 6. Developmental trajectories of CGE-, MGE- and LGE-derived neurons.

a, UMAP representation of all neurons from embryonic ages to P14 that will form the CTX–CGE GABA, CTX–MGE GABA and CNU–MGE GABA classes. Cells are coloured and labelled by subclass. b,c, Constellation plots showing all clusters using UMAP coordinates from a. Nodes are clusters that are coloured and labelled by subclass (b) or the proportion of age bins (c). The bubbles represent classes (b) and subclasses (c). d, UMAP representation of all neurons from embryonic ages to P14 that will form the OB–IMN GABA and CNU–LGE GABA classes. Cells are coloured and labelled by subclass. e, Constellation plot showing all clusters using UMAP coordinates from d. Nodes are coloured and labelled by subclass, and bubbles behind constellation are coloured by class. f, UMAP representation of all neurons from embryonic ages to P14 that will form the CNU–LGE GABA class. Cells are coloured and labelled by subclass. g, Constellation plot showing all clusters using UMAP coordinates from f. Nodes are clusters that are coloured by the proportion of age bins. The bubbles represent subclasses. The triangular schematic denotes the most granular hierarchical level shown in the panels (supertype). All class, subclass and region abbreviations are listed in Supplementary Table 1.

Extended Data Fig. 1. GABAergic neuronal type composition in different regions of the telencephalon.

(a) Heatmap showing the proportion of cells in each broad region of the telencephalon per GABAergic supertype. Triangular schematic denotes the most granular hierarchical level shown in the panel (ST: supertype). (b) Heatmap showing the proportion of cells in each supertype from 06 CTX-CGE GABA and 07 CTX-MGE GABA classes in each cortical layer and substructure of the hippocampal formation. (c-d) Constellation plots of the global relatedness between subclasses (c) or supertypes (d). Each subclass or supertype is represented by a disk, labelled by the subclass or supertype ID, and positioned at the subclass or supertype centroid in UMAP coordinates shown in Fig. 1b or c. The size of the disk corresponds to the number of cells within each subclass or supertype, and the edge weights correspond to the fraction of shared neighbours (see Methods) between subclasses or supertypes. In d, each supertype disk is coloured by the subclass it belongs to. Bubbles drawn around subclasses or supertypes outline the major classes. Triangular schematics denote the specific hierarchical level depicted in each panel (SC: subclass; ST: supertype).

Extended Data Fig. 2. Olfactory bulb GABAergic and immature neuronal cell types.

(a) UMAP representation of OB GABAergic and immature neuronal types, coloured and labelled by supertype. (b) Constellation plot of OB-IMN GABA clusters using UMAP coordinates shown in a. Nodes are clusters coloured by supertype and grouped in bubbles by subclass. (c) Dendrogram of OB-IMN GABA supertypes followed by bar graphs showing major neurotransmitter type and region distribution of profiled cells, followed by dot plot showing marker gene expression in each supertype from the 10xv3 dataset. Dot size and colour indicate proportion of expressing cells and average expression level in each supertype, respectively. (d) Schematic drawing of anatomical structure in MOB (left) and AOB (right). Abbreviations: RMS, rostral migratory stream; GrO, granular layer; IPl, internal plexiform layer; Mi, mitral layer; EPl, external plexiform layer; Gl, glomerular layer. (e-k) Representative MERFISH sections showing the location of OB subclasses 39 OB Meis2 Thsd7bGaba (e), 40 OB Trdn Gaba (f), 42 OB-out Frmd7 Gaba (g), 43 OB-mi Frmd7 Gaba (h), 44 OB Dopa-Gaba (i), 41OB-in Frmd7 Gaba (j), and 45 OB-STR-CTX Inh IMN (k). Cells are coloured and labelled by supertype. Triangular schematic denotes the most granular hierarchical level shown in the panels (ST: supertype).

Extended Data Fig. 3. Correspondence between the current transcriptomic taxonomy of OB-IMN GABA,CNU-LGE GABA, and CNU-HYa GABA classes and previously published ones.

Correspondence was determined by mapping cells from previously published datasets to the current taxonomy as described before. (a,b) Mapping of Tepe et al. (a) and Cebrian-Silla et al. (b) to the OB-IMN GABA class. (c,d) Mapping of Stanley et al. (c) and Chen et al. (d) to the CNU-LGE GABA class. (e,f) Mapping of Knoedler et al. (e) and Hochgerner et al., 2023 (f) to supertypes in the CNU-HYa class or the entire telencephalic GABAergic taxonomy. Triangular schematics denote the specific hierarchical level shown in each panel (ST: supertype; CL: cluster).

Extended Data Fig. 4. CGE-derived GABAergic neuronal types in the cerebral cortex.

(a) UMAP representation of all CGE clusters coloured and labelled by supertype. (b) Constellation plot of CGE clusters using UMAP coordinates shown in a. Cluster nodes are coloured by supertype and grouped in bubbles by subclass. (c) Dendrogram of CGE supertypes followed by bar graphs showing major neurotransmitter type, region distribution of profiled cells, dominant region (red dot), and number of cells within supertype, followed by dot plot showing marker gene expression in each supertype from the 10xv3 dataset. The dominant region was assigned if more than 70% of cells are from the assigned region. For the gene expression dot plot, dot size and colour indicate proportion of expressing cells and average expression level in each supertype, respectively. (d-g) Representative MERFISH sections showing the location of supertypes in CGE subclasses 46 Vip Gaba (d), 47 Sncg Gaba (e), 48 RHP-COA Ndnf Gaba (f), and 49 Lamp5 Gaba (g). Cells are coloured and labelled by supertype. Triangular schematic denotes the most granular hierarchical level shown in the panels (ST: supertype).

Extended Data Fig. 5. Correspondence of CGE and MGE GABAergic neuronal types with previously published cell-type taxonomies.

(a-b) CGE (a) and MGE (b) GABAergic cell types identified in this study are compared to cell types in CTX-HPF study and VISp Patch-seq study. The size of the dots corresponds to the number of overlapping cells in corresponding taxonomies. Columns are separated by supertypes, and rows are separated manually based on subclass in the corresponding dataset. Triangular schematics denote the most granular hierarchical level shown in the panels (CL: cluster).

Extended Data Fig. 6. Subclass and supertype marker genes within CTX-MGE, CNU-MGE, and CNU-LGE GABAergic neuronal types.

(a-b) Dendrogram of MGE (a) and CNU-LGE (b) supertypes followed by bar graphs showing major neurotransmitter type, region distribution of profiled cells, dominant region, and number of cells within supertype, followed by dot plot showing marker gene expression in each supertype from the 10xv3 dataset. The dominant region was assigned if more than 70% of cells are from the OLF-HPF-CTXsp regions. For the gene expression dot plot, dot size and colour indicate proportion of expressing cells and average expression level in each supertype, respectively. Triangular schematic denotes the most granular hierarchical level shown in the panel (ST: supertype).

Extended Data Fig. 7. Distribution of telencephalic cholinergic neurons.

(a) UMAP representation of all telencephalic GABAergic neurons as in Fig. 1b–d, cells in background are coloured classes that contain cholinergic neurons and foreground cells are coloured by supertype. Inserts show the cholinergic neurons belonging to the CNU-MGE GABA and LSX GABA classes, respectively, coloured by cluster. (b-d) Representative MERFISH sections showing cholinergic neurons coloured by cluster for supertypes 259 PAL-STR Gaba-Chol_1 (b), 260 PAL-STR Gaba-Chol_2 (c), and 307 LSX Nkx2-1 Gaba_2 (d). (e) Dot plot showing marker gene expression in each cholinergic cluster from the 10xv3 dataset. Dot size and colour indicate proportion of expressing cells and average expression level in each cluster, respectively. Triangular schematic denotes the most granular hierarchical level shown in the panels (CL: cluster).

Extended Data Fig. 8. GABAergic cell types of the lateral septum.

(a-b) UMAP representation of all LSX cells coloured by subclass (a) or supertype (b). (c) Constellation plot of LSX supertypes using UMAP coordinates shown in b. Nodes are coloured by supertype and grouped in bubbles by subclass. (d) Dendrogram of LSX supertypes followed by tiles showing major neurotransmitter type, followed by a heatmap showing the region distribution of profiled cells, then followed by dot plot showing marker gene expression in each supertype from the 10xv3 dataset. Dot size and colour indicate proportion of expressing cells and average expression level in each supertype, respectively. (e-j) Representative MERFISH sections showing the location of supertypes in LSX subclasses 67 LSX Sall3 Pax6 Gaba (e), 68 LSX Otx2 Gaba (f), 69 LSX Nkx2-1 Gaba (g), 70 LSX Prdm12 ve Gaba (h), 71 LSX Prdm12 do Gaba (i), and 72 LSX Sall3 Lmo1 Gaba (j). Triangular schematic denotes the most granular hierarchical level shown in the panels (ST: supertype).

Extended Data Fig. 9. GABAergic cell types of the CNU and anterior hypothalamus (HYa).

(a-b) UMAP representation of all cells in the CNU-HYa GABA class coloured and labelled by subclass (a) or supertype (b). (c) Constellation plot of CNU-HYa supertypes using UMAP coordinates shown in b. Nodes are coloured by supertype and grouped in bubbles by subclass. (d) Dendrogram of CNU-HYa supertypes followed by tiles showing major neurotransmitter type, followed by a heatmap showing the region distribution of profiled cells, then followed by dot plot showing marker gene expression in each supertype from the 10xv3 dataset. Dot size and colour indicate proportion of expressing cells and average expression level in each supertype, respectively. Triangular schematic denotes the most granular hierarchical level shown in the panels (ST: supertype).

Extended Data Fig. 10. Laminar distribution and gene expression gradients of MGE GABAergic neurons in cortex and hippocampal formation.

(a) Heatmap showing the proportion of cells in each layer or region of the isocortex and HPF for supertypes in the 52 Pvalb Gaba and 53 Sst Gaba subclasses. (b,c) Representative MERFISH sections showing the distribution of neurons across isocortex and HPF in select supertypes from subclasses 52 Pvalb Gaba (b) and 53 Sst Gaba (c). (d,e) Dot plots showing expression level of genes driving the gene expression gradient along the cortical depth for supertypes (ordered from deep to superficial) within the 52 Pvalb Gaba (d) and 53 Sst Gaba (e) subclasses. Dot size and colour indicate proportion of expressing cells and average expression level in each supertype, respectively. Genes labelled in green are shared between the two subclasses. (f, g) Representative examples of genes that drive the laminar gene expression gradient, plotted on the same MERFISH section as in panels b and c, shown for the 52 Pvalb Gaba (f) and 53 Sst Gaba (g) subclasses. Each cell is coloured by relative gene expression level. Triangular schematic denotes the most granular hierarchical level shown in the panels (ST: supertype).

Extended Data Fig. 11. Gene signatures defining shared gradients in D1 and D2 medium spiny neurons.

(a) Constellation plot of clusters showing the pairs of similar clusters between 61 STR D1 Gaba and 62 STR D2 Gaba subclasses. Clusters are represented by a disk coloured by cluster, labelled by cluster ID, and disks with a coloured border are highlighted exemplars in panels b to f. (b-f) Representative MERFISH sections showing five examples of STR D1 and STR D2 cluster pairs from panel a, and their spatial distribution patterns. Sections are coloured by cluster identity. (g-h) Gene expression dot plots of two major gene modules driving the spatial gradient among STR D1 (g) and STR D2 (h) clusters. Dot size and colour indicate proportion of expressing cells and average expression level in each cluster, respectively. Underneath the dot plot, a violin plot of the medial-lateral coordinate for each MERFISH cell per cluster is shown. (i-p) Based on the gene modules (light blue and dark blue) identified in panels g-h, a cumulative gene score was calculated using UCell. UMAPs showing CNU-LGE GABAergic neurons (i,j,m,n), and representative MERFISH sections (k,l,o,p), coloured by the light blue gene module score for STR D1 (i,k) and STR D2 (j,l) types, or coloured by the dark blue gene module score for STR D1 (m,o) and STR D2 (n,p) types. Triangular schematic denotes the most granular hierarchical level shown in the panels (CL: cluster).

Extended Data Fig. 12. Spatial gradients in LSX.

(a) Heatmaps showing expression of genes that drive the spatial gradients among subclasses in LSX in the top five gene modules. Each module contains genes that are both up- and down-regulated along the spatial gradient. (b-c) Gene signature score for these five modules is calculated for every cell and shown in the scRNA-seq UMAP representations (b) and representative MERFISH sections (c).

Extended Data Fig. 13. Developmental datasets integrated with the P56 Subpallium GABAergic neuron taxonomy.

(a,b) Comparison of UMI counts (a) and gene counts (b) per cell for the post-QC developmental and adult (10xv3) datasets. Boxplots show median, interquartile range and 1.5× interquartile range. Number of cells in each dataset: AIBS_E11.5_E14.5, n = 9,296; AIBS_P0, n = 54,247; AIBS_P4, n = 83,650; AIBS_P8, n = 94,535; AIBS_P12, n = 68,636; AIBS_P14, n = 76,784; AIBS_P56, n = 341,644; Allaway_2021, n = 18,131; Kaplan_2024, n = 26,344; LaManno_2021, n = 39,772; Lee_2022A, n = 18,200; Lee_2022B, n = 72,589; Mayer_2018A, n = 7,777; Mayer_2018B, n = 27,472; Turrero-Garcia_2021, n = 17,136. (c) UMAP representation of all cells across embryonic to P56 timepoints following scVI integration, coloured by dataset. (d) Confusion matrix between chronological age and predicted age (see Methods).

Extended Data Fig. 14. Comparison of cell type annotations between the subpallium GABAergic neuronal type taxonomy and published developmental studies.

(a-d) Correspondence of cell type annotations from published studies included in the developmental dataset and the current subpallium GABAergic neuronal type taxonomy. Cell type annotations from the current taxonomy are compared to the La Manno et al. dataset at supertype-to-cluster level (a) and class-to-class level (b). The current taxonomy is compared to the Turrero-Garcia et al. dataset at supertype-to-cluster level (c) and compared to the Kaplan et al. dataset at supertype-to-cluster level (d). Triangular schematics denote the specific hierarchical level shown in the panels (C: class, ST: supertype).

Extended Data Fig. 15. Transcription factor expression marking developmental lineages.

(a) UMAP representation of all cells across embryonic to P56 timepoints coloured by expression level of major lineage marker genes. The coloured dots next to each gene name show the adult cell classes that express that gene. (b) Representative developmental ISH (E13.5) and adult MERFISH sections showing expression of key TFs in GABAergic neurons. Genes marked with parentheses indicate imputed spatial gene expression pattern on MERFISH sections (see Methods).

Extended Data Fig. 16. Gene signatures of immature neuronal populations.

(a-c) Dot plots showing gene expression signatures for clusters in the 54 MGE Immature class (a), 55 LGE Immature class (b), and 56 CNU-HYa Immature class (c). Genes marked with purple dots are shown on a UMAP representation of all cells across embryonic to P56 timepoints coloured by expression level (d). Triangular schematic denotes the specific hierarchical level shown in the panels (CL: cluster).

Extended Data Fig. 17. Developmental trajectory of CGE- and MGE-derived neurons.

(a-d) UMAP representation of all neurons from embryonic ages to P14 that will form the 06 CTX-CGE GABA, 07 CTX-MGE GABA, and 08 CNU-MGE GABA classes, coloured by age (a), class (b), subclass (c), or dataset (d). UMAPs on the right side of panel a show cells in each age bin individually. (e) UMAPs showing expression of genes that mark the 51 Pvalb chandelier Gaba subclass (dashed oval). (f) UMAPs showing expression of genes that link the 50 Lamp5 Lhx6 Gaba subclass (dashed oval) to both MGE and CGE origins.

Extended Data Fig. 18. Gene expression gradient formation during development.

(a,b) Dot plots showing expression level of genes driving the gene expression gradient along the cortical depth identified in the P56 data within the Pvalb Gaba (a) and Sst Gaba (b) subclasses for ages P0-P2, P8, and P14. The genes and supertypes are ordered exactly as shown in Extended Data Fig. 10d, e. (c,d) Gene expression dot plots of two major gene modules driving the spatial gradient among STR D1 (c) and STR D2 (d) clusters identified in the P56 data for ages P0-P2, P4, P8, P12 and P14. The genes and supertypes are ordered exactly as shown in Extended Data Fig. 11g, h. Dot size and colour indicate proportion of expressing cells and average expression level in each supertype, respectively.

Extended Data Fig. 19. Developmental trajectory of LGE-derived neurons.

(a-b) UMAP representation of all neurons from embryonic ages to P14 that are derived from LGE and will populate the OB-IMN GABA and CNU-LGE GABA classes. UMAPs are coloured by age (a) or subclass (b). (c-d) UMAP representation of all neurons from embryonic ages to P14 that will form the CNU-LGE GABA class. UMAPs are coloured by age (c) or subclass (d). (e) Heatmap showing differentially expressed genes in the STR D1 and STR D2 trajectories across time. Eight gene modules were identified that show various modes of expression along and between subclasses over time. (f,i) Gene module scores marking different stages along the maturation path of D1 and D2 neurons. Gene modules (GM) 3 and 4 highlight STR D1 (f) and STR D2 (i) neurons respectively. (g,h,j,k) UMAP representation like in panels c-d coloured by major trajectory markers. (l-n) Gene module 5 contains genes highlighting the delayed maturation of STR D2 vs STR D1 neurons (l), such as two exemplar genes Hs6st2 (m) and Nrxn1 (n). (o-q) Gene module 7 contains genes whose expressions converge along the maturation trajectory of STR D1 and STR D2 neurons (o), such as two exemplar genes Tnr (p) and Slit3 (q). (r) Violin plot showing the transcriptomic distance between STR D1 and STR D2 subclass transcriptomes across the time course. Left panel: n for increasing age in the 061 STR D1 Gaba subclass: 120, 76, 4242, 7873, 8559, 12117, 35578, 14536 edges between 061 STR D1 Gaba and closest 062 STR D2 Gaba clusters. Right panel: n for increasing age in the 062 STR D2 Gaba subclass: 45, 52, 2604, 7224, 7700, 11195, 36193, 13549 edges between 062 STR D2 Gaba and closest 061 STR D1 Gaba clusters. Boxplots within violins show median, interquartile range and 1.5× interquartile range.

Extended Data Fig. 20. Developmental trajectory of LSX and CNU-HYa GABAergic neurons.

(a-e) UMAP representation of all neurons from embryonic ages to P14 that will form the 10 LSX GABA and 11 CNU-HYa GABA classes, coloured by class (a), subclass (b), age (c,d), and dataset (e). UMAPs in panel d show cells in each age bin individually. (f) UMAP representation as in panels a-e coloured by expression level of subclass marker genes. The coloured dots next to each gene name show the subclasses expressing that gene.