Extended Data Table 2.
Cluster IDs of E35 ferret cerebral cortical cells analyzed by single-cell RNA sequencing. The three clusters highlighted in blue represent the largest proportional changes with empirical FDR < 0.01, and are similarly indicated in Figure 3. Statistical analysis was performed by two-tailed Chi-square test.
| Color | Cluster ID |
Top 10 Marker Transcripts | Inferred Cell Type | Cell Count
in Aspm+/− |
Cell Count
in Aspm−/− |
Proportion
of Aspm+/− |
Proportion
of Aspm−/− |
Fold- change in proportion |
Empirical P- value |
|---|---|---|---|---|---|---|---|---|---|
| RG1 | TOP2A; HMGB2; CENPF; CENPE; TPX2; XLOC_000183; 2810417H13Rik; SMC4; XLOC_036181; KIF11 | Cycling radial glial progenitors | 803 | 1,661 | 10.5% | 12.1% | +15% | 0.0002 (FDR<0.01) | |
| RG2 | VIM; HES1; SLC1A3; GDPD2; SFRP1; PON2; PTN; SMPDL3A; NES; PAX6 | Interphase radial glial progenitors | 495 | 800 | 6.5% | 5.8% | −10% | 0.0696 | |
| IP | NRN1; PTPDC1; TENM4; ELAVL4; ROBO2; FBXW7; IGFBP2; NELL2; PRKX; TTC28 | Intermediate progenitors | 686 | 1,603 | 9.0% | 11.7% | +30% | 0.0002 (FDR<0.01) | |
| EN1 | SYT4; CSRP2; NEUROD6; NEUROD2; UNC5D; NTM; NSG2; LIMCH1; SORBS2; ISLR2 | Upper-layer excitatory neurons | 2,203 | 3,490 | 28.8% | 25.4% | −12% | 0.0002 (FDR<0.01) | |
| EN2 | NEFM; FEZF2; NEFL; GRIA2; GUCY1B3; DYNC1I1; ARPP21; NEUROD6; B3GALT2; KCTD12 | Deep-layer excitatory neurons | 981 | 1,053 | 12.8% | 7.7% | −40% | 0.0002 (FDR<0.01) | |
| EN3 | RELN; LHX1; NDNF; TP73; NHLH2; VSNL1; ENSMPUG00000012124; PLCL1; ENSMPUG00000009767; SEMA6A | Cajal-Retzius cells | 103 | 227 | 1.3% | 1.7% | +23% | 0.0704 | |
| IN1 | PBX3; MEIS2; XLOC_008478; ENSMPUG00000024751; INA; MAP1B; ATP1B1; XLOC_021005; RUNX1T1; JAKMIP2 | Immature inhibitory neurons | 591 | 1,167 | 7.7% | 8.5% | +10% | 0.0444 | |
| IN2 | SST; XLOC_014564; PDZRN4; NXPH1; NXPH2; SYT1; XLOC_026835; GRIA1; ARX; PDE4DIP | SST interneurons | 734 | 1,568 | 9.6% | 11.4% | +19% | 0.0002 (FDR<0.01) | |
| IN3 | XLOC_026835; DLX1; XLOC_026893; CCDC88A; ZNF704; PFN2; EPHA5; XLOC_007250; INA; NR2F1 | Ventral/inhibitory progenitors | 710 | 1,521 | 9.3% | 11.1% | +19% | 0.0002 (FDR<0.01) | |
| ENDO1 | APOA1; COL4A1; CALD1; SPARC; FN1; IGFBP7; XLOC_010971; ENSMPUG00000012145; LAMA4; MGP | Endothelial cells | 122 | 210 | 1.6% | 1.5% | −4% | 0.7418 | |
| ENDO2 | SPARCL1; LYZ; PECAM1; IFNAR1; SPARC; IFI27; XLOC_010971; EMB; S100A6; IGFBP7 | Endothelial cells | 113 | 150 | 1.5% | 1.1% | −26% | 0.0166 (FDR<0.05) | |
| OPC | APOD; XLOC_017682; SCRG1; DBI; SPARCL1; PDGFRA; SERPINE2; ENSMPUG00000011077; PTPRZ1; LHFPL3 | Oligodendrocyte precursors | 48 | 170 | 0.6% | 1.2% | +97% | 0.0002 (FDR<0.01) | |
| MG | ENSMPUG00000001122; C1QC; C3; RGS10; XLOC_039347; CCL8; XLOC_039690; ZFP36; CCL4; SPP1 | Microglia | 56 | 105 | 0.7% | 0.8% | +4% | 0.7234 |