Table 3

Differential gene expression analysis between E16.5 DG/cortex RPs and E14 GE RPs (related to Fig. 5)

DE geneAverage logFCAdjusted p value
Dmrta20.636.00E-19
Aldoc0.981.07E-15
Pax60.685.02E-13
Btg10.762.65E-18
Tfap2c0.731.45E-27
Neurog21.086.34E-18
Fezf20.654.26E-18
E130114P18Rik0.873.97E-22
Emx10.761.16E-29
Dok50.922.08E-37
Cdon0.438.34E-04
Eomes0.403.94E-02
Nfib0.661.24E-14
Ccdc801.229.16E-45
Fam210b0.647.33E-07
Gm37640.681.43E-14
Nfix1.053.33E-23
Emx20.552.61E-04
Kcnq1ot10.551.90E-06
Hmgn30.652.46E-18
Tcf.40.563.15E-12
Gm112660.411.15E-06
Tgfb20.644.88E-19
Mt11.648.65E-38
Mt21.758.69E-29
Fut90.548.48E-10
Pid1−0.561.30E-12
Dlx2−1.204.90E-25
Olig2−0.822.76E-15
Rbp1−1.921.43E-38
Gsx2−0.635.28E-14
Epha3−0.772.77E-21
Meg3−1.483.26E-26
Six3−0.552.87E-13
Nell2−0.675.69E-15
Lmo4−0.436.56E-06
Chic2−0.452.30E-07
Dlx1−0.876.63E-16
Ckb−1.114.64E-44
Ascl1−0.739.94E-06
Nkx2-3−0.502.08E-11
H19−0.582.12E-11
Dlk1−0.352.93E-04
Zfp36l2−0.335.87E-05
Enho−0.332.88E-04
Dtnbp1−0.381.02E-05
Rgcc−0.881.15E-17
Zeb2−0.534.91E-10
Ttc9b−0.292.04E-05
Metrn−0.373.42E-05
Helt−0.408.66E-03
Sall3−0.362.27E-05
Asrgl1−0.308.89E-03
Pak3−0.511.74E-08
Mest−0.955.72E-09
Hat1−0.709.08E-15
Dleu7−0.491.59E-05
  • A total of 117 genes was previously shown to be differentially expressed between E14 cortical RPs and E14 GE RPs (average difference > 0.5, FWER < 0.05) in Borrett et al. (2020). Of these, 54 were enriched in cortical RPs and 63 were enriched in GE RPs. These 117 genes were interrogated for their relative levels of expression in E16.5 DG RPs and E14 GE RPs (from the dataset shown in Fig. 5A). This analysis identified 26 (of 54) cortically enriched genes that were also significantly enriched in E16.5 SGZ RPs relative to E14 GE RPs, and 31 (of 63) GE-enriched genes that were also significantly enriched in E14 GE RPs relative to E16.5 SGZ RPs. These 57 genes are shown, as are the log fold changes in expression and adjusted p values (FWER < 0.05). Positive fold change values represent enriched expression in E16.5 SGZ RPs relative to E14 GE RPs and negative fold change values indicate enriched expression in E14 GE RPs relative to E16.5 SGZ RPs. These same 57 genes are depicted in the heatmaps in Figure 5C,D.