Supplemental Figure 1 Emx1IREScre-mediated recombination in specific forebrain domains at mid-gestation. A-M An X-gal stained E12.5 Emx1^IREScre;R26R embryo was sectioned at 10 mm in the coronal plane. AEP, anterior entopeduncular area; amyg, amygdala; CA, central amygdala; ch, choroid plexus primordium; di, diencephalon; DP, dorsal pallium; EMT, eminentia thalami; hem, cortical hem; MA, medial amygdala; MGE, medial ganglionic eminence; MP, medial pallium; mes, mesencephalon; LGE, lateral ganglionic eminence; LP, lateral pallium; POA, preoptic area; OT, olfactory tract; p2, prosomere 2; pspb, pallial-subpallial boundary; Sp, pallial septum; Ssp, subpallial septum; VP, ventral pallium; VTh, ventral thalamus. R-U Four different X-gal stained E12.5 Emx1^IREScre; R26R embryos showing minimal variability of recombination. Asterisk in T labels an island of negative cells intercalated in the lateral pallium.

Supplemental Figure 2 Recombination in the adult Emx1^IREScre;R26R and Emx1^IREScre;Z/AP brain. A-M 40 mm sections stained with X-gal from an adult Emx1^IREScre;R26R brain, showing extensive recombination in pallial-derived structures but not in subpallial-derived structures. N X-gal stained 40 mm coronal section of Emx1^IREScre;Z/AP brain, showing extensive recombination throughout the cortex and hippocampus but not in the blood vessels in these structures. Abbreviations: AA, anterior amygdaloid area; ac, anterior commissure; ACo, anterior cortical amygdaloid nucleus; AHip, amygdalohippocampal area; AON, anterior olfactory nucleus; AONd, anterior olfactory nucleus dorsal; AONl, anterior olfactory nucleus lateral; AONm, anterior olfactory nucleus medial; AONv, anterior olfactory nucleus ventral; APir, amygdalopiriform area; BL, basolateral amygdala; BM, basomedial amygdala; Bst, bed nucleus of stria terminales; C, central amygala; Cb, cerebellum; cc, corpus callosum; ch, choroid plexus; Cing.Cx, cingulate cortex; CLdl, dorsolateral claustrum; CLvm, ventromedial claustrum; Cx, cortex; CxA, cortex-amygdala transition zone; DP, dorsal pallidum; DTr, dorsal transition zone; DTT, dorsal tenia tectum; EPd, dorsal endopiriform nucleus; EPv, ventral endopiriform nucleus; ERCx, ectorhinal cortex; f, fimbria; FCx, frontal cortex; fx, fornix; H, hippocampus; Hy, hypothalamus; I, intercalated amygdaloid nucleus; Ins, insular cortex; L, lateral amygdala; lay.II, layer II of piriform cortex; lot, lateral olfactory tract; LP, lateral pallidum; LS, lateral septal nucleus; LSD, lateral septal nucleus dorsal; LSI, intermediate lateral septal nucleus; M, medial amygdala; Mpd, medial amygdaloid nucleus posterodorsal; Mpv, medial amygdaloid nucleus posteroventral; NAOT, bed nucleus of the accessory olfactory tract; NLOT (2), nucleus of lateral olfactory tract, layer II; OB, olfactory bulb; OT, olfactory tubercle; Pal, pallidum; PCol, posterolateral cortical amygdaloid nucleus, PCom, posteromedial amygdaloid nucleus; PirCx, piriform cortex; PLd, paralamboid septal nucleus dorsal; Pn, pontine nuclei; SC, superior colliculus; Ssp, subpallial septum; St, striatum; Th, thalamus; TS, triangular septal nucleus; VP, ventral pallidum; VTT, ventral tenia tectum.

Supplemental Figure 2