Table 1.
Cell-type census of 69 populations of spinal cord neurons.
| Cluster | Lamina | % | NT | Family | Individual Markers | Putative Lineage | ||
|---|---|---|---|---|---|---|---|---|
| MN-alpha | 9 | 1.1 | Chat | MN | Spp1 | Poln | Tns1 | MN |
| MN-gamma | 9 | 0.5 | Chat | MN | Esrrg | Htr1f | Tns1 | MN |
| PGC | 7-IML | Chat | MN | Gfra3 | Nos1 | Fbn2 | MN | |
| CSF-cN | 10 | 0.3 | Slc6a1 | CSF-cN | Pkd2l1 | V2b.2/V2b.4 | ||
| Excit-1 | 1/2o | 0.6 | Slc17a6 | Cpne4 | Dach2 | (Cck) | dI3.3/dI5 | |
| Excit-2 | 1/2o/2i | 3.7 | Slc17a6 | Cpne4 | Prkcg | (Rorb) | dI5.4 | |
| Excit-3 | 1/2o/2i | 3.8 | Slc17a6 | Prkcg | (Cck) | Calb1 | dI5.4 | |
| Excit-4 | 2i/3 | 2.8 | Slc17a6 | (Prkcg) | Nts | Calb1-hi | dI5.4 | |
| Excit-5 | 2i/3/4 | 3.2 | Slc17a6 | Maf | Cck | dI5.4 | ||
| Excit-6 | 3/4 | 2.4 | Slc17a6 | Maf | Rorb | Cpne4 | dI5.4/dI5.5 | |
| Excit-7 | N/A | N/A | Slc17a6 | Maf | Dcx | (vGlut3) | dI5.4/dI5.5 | |
| Excit-8 | 1/2 | 1.4 | Slc17a6 | Reln | Trhr | (Car12) | (Grp) | dI3.3/dI5.4 |
| Excit-9 | 1/2/3 | 1.7 | Slc17a6 | (Reln) | Grp | Calb2 | dI5.4/dI5.5 | |
| Excit-10 | 1/2 | 2 | Slc17a6 | Reln | Car12 | Nmur2 | dI5.4 | |
| Excit-11 | N/A | 0 | Slc17a6 | Reln | Car12 | Gabra2 | dI5.4 | |
| Excit-12 | 1/2 | 0.2 | Slc17a6 | Rreb1 | Satb1 | Zim1 | dI5.5 | |
| Excit-13 | 2i/3 | 0.7 | Slc17a6 | Rreb1 | Nmur2 | (Satb1) | dI5.5 | |
| Excit-14 | 1/2o | 1.7 | Slc17a6 | Sox5 | Col5a2 | (dI5) | ||
| Excit-15 | 1/2/3 | 0.2 | Slc17a6 | Sox5 | Col5a2 | Enpp1 | (dI5) | |
| Excit-16 | 1/2o (2i-4) | 6.5 | Slc17a6 | Sox5 | Col5a2 | Enpp1 | Tac1 | (dI5) |
| Excit-17 | N/A | N/A | Slc17a6 | Sox5 | Dcx | (dI5) | ||
| Excit-18 | 1/2o (2i-4) | 2.7 | Slc17a6 | Sox5 | Nmu | (Tac2) | (dI5) | |
| Excit-19 | 2i (3/4) | 1.9 | Slc17a6 | Sox5 | Tac2 | (Nmu) | dI5.4/dI5.5 | |
| Excit-20 | 4/5 | 2 | Slc17a6 | Megf11 | Mdga1 | dI2.1/dI5.5 | ||
| Inhib-1 | 3 (1-4) | 7.4 | Slc6a1 | Rorb | Sorcs3 | (Nppc) | (Runx2) | dI4.3 |
| Inhib-2 | 3 (1-4) | 10.3 | Slc6a1 | (Rorb) | Adamts5 | Klhl14 | Sorcs3 | dI4.3 |
| Inhib-3 | 1-4 | 3 | Slc6a1 | Rorb | Nppc | Nrgn | dI4.3 | |
| Inhib-4 | 1/2o/2i | 0.4 | Slc6a1 | Rorb | Rxfp2 | dI4.3 | ||
| Inhib-5 | 1/2o (3) | 1 | Slc6a1 | Rorb | dI4.3 | |||
| Inhib-6 | 3/4 (1/2o) | 1.3 | Slc6a1 | Cdh3 | dI4.4 | |||
| Inhib-7 | 2i/3 (1-4) | 3.6 | Slc6a1 | Cdh3 | Kcnip2 | Pvalb | dI4.4 | |
| Inhib-8 | 3/4 | 0.5 | Slc6a1 | (Cdh3) | Klhl14-hi | dI4.4 | ||
| Inhib-9 | 1/2o (2i/3) | 1.6 | Slc6a1 | Pdyn | (Rorb) | (Rspo3) | dI4.1/dI4.4 | |
| Inhib-10 | 3 (1-5) | 9.7 | Slc6a1 | Pdyn | Gal | Mlxipl | Rspo3 | dI4.1/dI4.4 |
| Inhib-11 | 1/2o/2i/3 | 0.9 | Slc6a1 | Pdyn | Gal | (Rorb) | Nrgn | dI4.1/dI4.4 |
| Inhib-12 | 1/2o/4 | 1.8 | Slc6a1 | Npy | (Vgf) | dI4.6 | ||
| Inhib-13 | 1/2o/2i | 2.1 | Slc6a1 | Npy | Qrfpr | dI4.6 | ||
| Inhib-14 | 4 | 0.1 | Slc6a1 | Chat | Slc6a5 | Nos1 | dI4.1/dI4.6 | |
| Excit-21 | 4/lat 5 | 0.5 | Slc17a6 | ME/Lmx1b | Zfhx3 | Nms | dI5.5 | |
| Excit-22 | 4/5/6 | 0.1 | Slc17a6 | ME/Lmx1b | Zfhx3 | dI3.3/dI5.5 | ||
| Excit-23 | 4/med 5 | 1.2 | Slc17a6 | ME/Lmx1b | Nfib | Cep112 | (dI5) | |
| Excit-24 | 4/5/6 | 0.7 | Slc17a6 | ME/Lmx1b | (Nfib) | (Cep112) | (dI5) | |
| Excit-25 | 4/5/6 | 0 | Slc17a6 | ME/Lmx1b | Nfib | Prox1 | (dI5) | |
| Excit-26 | 4 | 0.1 | Slc17a6 | ME | Nfib | (Prox1) | (Satb1) | (dI1/dI2) |
| Excit-27 | 4/5 | 1.3 | Slc17a6 | ME | Adamts2 | Cep112) | (dI2) | |
| Excit-28 | 10 | 0.1 | Chat | ME | Pitx2 | Pou6f2 | Onecut2 | V0* |
| Excit-29 | 5/6 | 0.3 | Slc17a6 | ME | Onecut2 | Pmfbp1 | (V0) | |
| Excit-30 | 5 | 0.8 | Slc17a6 | CC# | Gbx2 | Neurod2+ | Pou6f2 | V2a.1 |
| Inhib-15 | med 5 | 1.1 | Slc6a5 | MI | Prox1 | Gabra1 | Nfib | V1.7 |
| Inhib-16 | med 5 | 0.6 | Slc6a5 | MI | Gpc3 | (Rorb) | Sema5b | dI4.6 |
| Inhib-17 | N/A | N/A | Slc6a5 | MI | Satb2 | dI4.4/dI4.6/(dI6) | ||
| Inhib-18 | 5/6 | 0.5 | Slc6a5 | MI | Sema5b | dI4 | ||
| Inhib-19 | med 5 | 0.5 | Slc6a5 | MI | Ccbe1 | Pou6f2 | dI4.4 | |
| Inhib-20 | 5/6 | 1 | Slc6a5 | MI | Tfap2b | dI4.6/V1.1/(dI6) | ||
| Inhib-21 | 4/med 5 | 0.8 | Gad2 | MI | Nfib | Pax6 | dI4.6/V1.6/(dI6) | |
| Excit-31 | 6/7/8 | 0.3 | Slc17a6 | VE | Lhx9 | Gm26673 | Syt2 | (dI1/dI2) |
| Excit-32 | 6/7/8 | 0.4 | Slc17a6 | VE | Lhx9 | Prlr | Mdga1 | dI1/dI2/dI3 |
| Excit-33 | N/A | N/A | Slc17a6 | VE | Lhx9 | dI2.1 | ||
| Excit-34 | 6/7/8 | 0.4 | Slc17a6 | VE | Bnc2 | Pou6f2 | Lhx2 | dI1/dI2 |
| Excit-35 | 6/7 | 0.5 | Slc17a6 | VE | Vsx2 | Pou6f2 | Vamp1 | V2a* |
| Excit-36 | 6/7 | 0.3 | Slc17a6 | VE | Vsx2 | Esrrg | (Gm26673) | dI1/dI2/V2a |
| Excit-37 | 7 | 0.8 | Slc17a6 | VE | Vsx2 | Shox2* | V2a* | |
| Excit-38 | N/A | N/A | Slc17a6 | VE | Sim1 | Rnf220 | V3* | |
| Inhib-22 | 7 | 0.1 | Slc6a5 | VI | Foxp2 | (Esrrb) | (dI6)/V1.3 | |
| Inhib-23 | 7/8 | 0.6 | Slc6a5 | VI | Foxp2 | Esrrbb+ | Gm26673 | (dI6)/V1.3 |
| Inhib-24 | 7 | 0.6 | Slc6a5 | VI | Pou6f2 | Nr5a2 | V1 | |
| Inhib-25 | 7/8 | 1.1 | Slc6a5 | VI | Esrrb | (Pvalb) | (dI6)/V1 | |
| Inhib-26 | ventral 7 | 0.5 | Slc6a5 | VI | Chrna7 | Calb1 | (Pvalb) | V1.1/V1.2 |
| Inhib-27 | 7 | 0.3 | Slc6a5 | VI | Foxp2 | (Gata3) | Pax2-hi | (dI6)/V1/V2b |
The lamina, prevalence, neurotransmitter marker gene, family, individual marker genes, and putative embryonic lineage for each neuronal cluster are shown. The clusters are color-coded to correspond approximately to their color in Fig. 2a. The prevalence of each cluster was determined by counting the confidently assigned cells of each type based on RNA in situ hybridization on sections from three animals and are presented as the percent of the total number of confidently assigned neurons. Genes in parenthesis are expressed at lower levels. Genes in gray were not validated (due to probe failure, being present only in postnatal animals, or were not included in the analysis). + denotes relatively higher expression. # denotes a possible identity of Clarke’s column (CC). * denotes a marker that was validated using RNAScope V2 but did not work in the RNAScope Hiplex assay.