Nature Methods: doi: /nmeth Supplementary Figure 1. Identification of candidate factors for the generation of inhibitory neurons.

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1 Supplementary Figure 1 Identification of candidate factors for the generation of inhibitory neurons. (a) Tuj1 + cells derived from human ES cells using different transcription factors 3 days after induction. Scale bars, 50 μm. (b) Schematic

2 representation of the strategy to test candidate GABAergic neuron-inducing factors. (c) Example traces recorded from in cells generated in different conditions. Left box: AMPAR-mediated spontaneous excitatory postsynaptic currents (sepsc) recorded from an example cell (Ngn2-iN cell). Expanded view of events reveals fast kinetics (middle). Center box: GABAR-mediated spontaneous inhibitory postsynaptic currents (IPSCs, top) with slower kinetics (middle) recorded from an example cell (AM+Dlx2-iN cell). Right box: Spontaneous EPSCs with fast kinetics and spontaneous IPSCs with slower kinetics recorded from an example cell (AM+Dlx5-iN cell). (d) Representative traces of spontaneous postsynaptic currents (spscs) with fast kinetics as recorded from an Ngn2+EGFPexpressing neuron (red, i), or spscs with slow kinetics as recorded from an AM+Dlx2-expressing neuron (blue, ii), that were blocked by NBQX (50 μm, AMPAR-antagonist) or picrotoxin (50 μm, GABA AR-antagonist), respectively. Insets = expanded views of boxed areas (dotted lines). (e) Bar-graphs show the average amplitude (top panels) and decay (bottom panels) of sepscs (red) and sipscs (blue) in cells infected with indicated transcription-factor combinations. Bar-graphs represent mean values ± SEM (n = 5-7 cells). Filled circles represent values measured from individual cells. Asterisks (red) indicate absence of EPSC events in AM+Dlx2-expressing neurons.

3 Supplementary Figure 2 Transcription factor combination AMD induces the differentiation of human pluripotent stem cells into a homogenous population of GABAergic neurons with high yield and reproducibility. (a) Representative traces of sipscs recorded from AMD-iN cells generated from three different human pluripotent stem cell lines. (b) AMD-iN cells generated from different cell lines show similar intrinsic properties in terms of membrane capacitance (C m, bi), inputresistance (R m, bii), and the average amplitude and frequency of the sipscs (biii and biv, respectively). Data are presented as mean ± SEM (one-way ANOVA, p > 0.05, n = 18 cells/condition), and filled circles represent values measured from individual cells.

4 Supplementary Figure 3 RNA-seq analysis of AMD-iN cells reveals expression of genes characteristic of different forebrain inhibitory neuron subtypes. (a-d) Shown are human-specific RPKM expression values for the indicated genes in AMD-iN cells 32 days after transgene induction and co-cultured with mouse glia for 4 weeks. Total RNA was collected and sequenced, but only human-specific reads were considered. DA, dopaminergic; Glu, glutamatergic; ACh, cholinergic; cin, cortical interneuron. Data are represented as mean of two biological replicates and the filled circles represent values measured from the 2 experiments.

5 Supplementary Figure 4 Detection of GABAergic neuron subtype markers in 5 WPI AD-iN cells. (a) The robust generation of GABAergic neurons expressing CR, CB and SST from different human ES and ips cells using Ascl1 and Dlx2. (b) ISL1 was observed in ~ 20% of the AD-iN cells and specific staining of NR2F2 in a small fraction of AD-iN cells (<2%) was detected (c). The bar graph shows the percentage of MAP2 positive cells that also express ISL1. Scale bar: 50 µm.

6 Supplementary Figure 5 Notch inhibitor enhanced the morphologic complexity of AD-iN cells.

7 (a) Schematic diagram represents experimental strategy for treating and characterizing cellular phenotype resulting from DAPT treatment in human neurons. (b-c) Brief DAPT treatment (3 or 4 days) at early stage during neuronal induction did not exhibit any effect on the neuronal morphology of AD induced neuronal cells revealed by MAP2 immunofluorescence. However, the mean process length of in cells significantly increased from day 4 to day 5 after transgene induction independent of DAPT treatment. (d-g) Whereas brief DAPT treatment during day 2-7 after transgene induction was sufficient to improve the complexity of the neuron morphology in terms of the max process length and the total neurite outgrowth (e, g), continuous DAPT treatment from day 2 onwards was necessary to further increase the number of branches (d).

8 Supplementary Figure 6 Ascl1 and Dlx2 induction generates mature neurons that form functional inhibitory synapses. (a) Spontaneous action potentials (APs) recorded from AD-iN cells, as replated on mouse glia at one week post-induction (WPI) and co-cultured for additional 4 (red, left) to 6 (blue, right) weeks (i); Representative traces (left) and average values (means ± SEM, n = 10

9 cells, right) of voltage-gated Na + and K + currents recorded from AD-iN cells at 6 weeks after glia co-culture (ii). (b) Immunoblot analyses of proteins extracted from AD-iN cells co-cultured with mouse glia cells or mouse glia only. Proteins are identified on the left (b-actin, GFAP, MAP2, Gephyrin, VELI, Munc18, Cask and SYT1 (Synaptotagmin-1). (c) Representative image showing vgat and Synapsin 1 (SYN1) expression in AD-iN cells co-cultured with mouse glia. (d) Representative traces of sipscs (blue trace, i) and extracellular stimulation-induced evoked IPSCs (blue trace, ii), as recorded from AD-iN cells 7 WPI, and were subsequently blocked by 50 µm picrotoxin (red traces, i and ii), a pharmacological blocker of GABA ARs.

10 Supplementary Figure 7 Continuous expression of AMD for 14 days was sufficient to induce neuronal cells with complex morphology and expressing synaptic marker SYN1. AMD-treated human ES cells where co-cultured with mouse glia from 7 days after AMD-induction. Doxycycline was withdrawn at different time (days after AMD-induction as indicated in the upper-left corner of each image). Immunofluorescence analysis was performed on day 28.

11 Supplementary Figure 8 Long term stability of the GABAergic fate and continuous maturation of AD-iN cells in vivo. (a,b) Representative image of an AD-iN cell graft in the mouse cortex 2 weeks post transplantation (w.p.t.). Transplanted cells were detected with EGFP (green) and human nuclei antibodies (blue) and expressed high levels of DCX (magenta). (b) Individual human DCX-positive cells show migrating morphologies. (c-e) After 3 months post transplantation (m.p.t.) we observed robust GABA and NeuN staining in the grafted cells. We also detected an increased number of NeuN+ cells over time.

12 Supplementary Figure 9 AMD-induced inhibitory neurons for human neurological disease modeling. (a) Sequence of shrnas targeting human Collybistin mrna. (b) Patch-clamp configuration for postsynaptic recordings performed on in cells expressing Collybistin shrnas (EGFP-positive). Collybistin KD in cells were co-cultured with Ngn2-induced human neurons (EGFP-negative, black arrowheads). Left, bright-field; Middle, EGFP-fluorescence view; and Right, as both views merged. Rec: recording electrode; Scale bars: 15 μm. The lower panel shows representative traces of AMPAR-mediated sepscs recorded from control (Ctrl, black) vs. Collybistin shrna #4 expressing (Sh#4, brown) neurons. (c) Cumulative plots (left) and average graphs (right) representing mean ± SE values of sepsc amplitude (i, top) and event frequency (ii, bottom), for control vs. Collybistin shrna #4 infected neurons. (d) Cumulative plots (left) and average values (mean ± SE, right) of intrinsic membrane properties: membrane capacitance (Cm, i), input resistance (Rm, ii), and resting membrane potential (Vm, iii), as recorded from control (Ctrl, black) vs. Collybistin shrna #4 expressing (Sh# 4, brown) human neurons. For cumulative plots, color-matched connected circles represent average values of corresponding parameters recorded from individual cells. For all experimental approaches, the numbers inside average bar-graphs indicate total number of cells recorded / number of independent batches. Statistical significance was tested by twotailed, unpaired, Student s t-test (ns = not significant, P > 0.05).

13 Supplementary Figure 10 Analysis of different transcription factor combinations confirmed that Ascl1 and Dlx2 are sufficient to generate SST-, CALB1(CB)-, CALB2(CR)-, VIP- and RELN-expressing cells. qrt-pcr analysis was performed for indicated genes using AD-iN cells or in cells generated by AD plus indicated factors. Expression levels (expressed as Ct values) are color coded as shown. In general, all the AD plus 1 conditions generated GABAergic neuron populations similar to those induced by AD or AD with Myt1l. All conditions generated in cells that robustly expressed SST, CALB1, SYN1 and vgat. Whereas the expression levels of PVAL and NPY are less prominent and more variable.

14 Supplementary Table 1. Antibodies used in this study Antibody Vendor Catalog# Calbindin (CB) Swant Calretinin Swant 6B3 2 Somatostatin Bachem T DARPP32 SCBT sc TTF1(NKX2-1) Invitrogen ISLET1 DSHB 39.3F7 2 Pan DLX gift from Yury M. Morozov 5 NeuN Millipore MAB377 2 GAD1 Millipore MAB GAD2 DSHB GAD6 6 Synapsin-1 Synaptic System DCX Cell Signaling 4604S 8 OLIG2 Millipore AB TUJ1 Covance MMS-435P 9 TUJ1 Covance MRB-435P 9 VGAT Synaptic System Human nuclei antigen Millipore MAB GFP Aves Labs GFP COUPTFII Perseus Proteomics PP-H MAP2 Abcam AB MAP2 Sigma Aldrich M GABA Sigma Aldrich A

15 Supplementary Table 2. TaqMan Gene Expression Assays from Thermo- Fisher Scientific (former Invitrogen) used in this study Gene Assay ID Gene Assay ID GAPDH Hs _g1 SST_A1 Hs _m1 NES Hs _g1 SST_A2 Hs _m1 SOX1 Hs _s1 VIP_A1 Hs _m1 OLIG2 Hs _m1 VIP_A2 Hs _m1 TUBB3 Hs _g1 NPY Hs _m1 SYN1 Hs _m1 NOS Hs _m1 vglut1 Hs _m1 NTR3A Hs _m1 vgat Hs _m1 CCK Hs _m1 GAD1 Hs _m1 RELN Hs _m1 GAD2 Hs _m1 NKX2.1 Hs _m1 GAT1 Hs _m1 LHX6 Hs _gH GAT2 Hs _m1 ZEB2 Hs _g1 GAT3 Hs _m1 SOX6 Hs _m1 DLX1 Hs _m1 SATB1 Hs _m1 DLX5 Hs _m1 CXCR4 Hs _s1 DLX6 Hs _m1 SP8 Hs _g1 PVALB_A1 Hs _m1 NR2F2 Hs _m1 PVALB_A2 Hs _m1 EMX1 Hs _m1 CALB1 Hs _m1 LHX8 Hs _m1 CALB2 Hs _m1 References 1. Schurmans, S. et al. Impaired long-term potentiation induction in dentate gyrus of calretinin-deficient mice. Proc. Natl Acad. Sci. 94, (1997). 2. Nicholas, C. R. et al. Functional maturation of hpsc-derived forebrain interneurons requires an extended timeline and mimics human neural development. Cell Stem Cell 12, (2013). 3. Victor, M. B. et al. Generation of Human Striatal Neurons by MicroRNA- Dependent Direct Conversion of Fibroblasts. Neuron 84, (2014). 4. Wang, P.-H., Wang, H.-C. & Tsai, C.-C. Estrogen replacement in female lung cancer during gefitinib therapy. Jpn. J. Clin. Oncol. 39, (2009). 5. Morozov, Y. M., Torii, M. & Rakic, P. Origin, early commitment, migratory routes, and destination of cannabinoid type 1 receptor-containing interneurons. Cereb Cortex 19 Suppl 1, i78 89 (2009).

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