Figure 3. SYNGAP1 haploinsufficiency disrupts the organization of the developing cortical plate.

A. Two-month-old Patient^Corrected and Patient^p.Q503X organoids expressing SOX2 and DAPI.

B. VZ thickness of Patient^p.Q503X and Patient^corrected organoids. Two-tailed t-test on n=132 VZs from Patient^corrected organoids and n=107 VZs from Patient^p.Q503X organoids from 4 independent experiments . Dots represent individual VZs. P value <0.0001 . Data shown as mean ± SD.

C. VZs area of Patient^p.Q503X and Patient^Corrected organoids. Two-tailed t-test on n=132 Patient^corrected and n=106 Patient^p.Q503X VZs from 4 independent experiments . Dots represent individual VZs. P value <0.0001 . Data shown as mean ± SD.

D. VZs number of Patient^p.Q503X and Patient^Corrected organoids. Two-tailed t-test on n=7 Patient^corrected and n=7 Patient^p.Q503X organoids from 4 independent experiments . Dots represent the mean number of VZs per ROI in individual organoids. P value <0.0001 . Data shown as mean ± SD.

E. Two-month-old 03231^Control and 03231^p.Q503X expressing SOX2 and DAPI.

F. VZ thickness of 03231^p.Q503X and 03231^Control organoids. Two-tailed t-test on n=68 03231^Control and n=111 03231^p.Q503X VZs from 4 independent experiments. Dots represent individual VZs. P value = 0.0078 . Data shown as mean ± SD.

G. VZs area of 03231^p.Q503X and 03231^Control organoids. Two-tailed t-test on n=84 03231^Control and n=68 03231^p.Q503X VZs from 4 independent experiments. Dots represent individual VZs. P value = 0.0046 . Data shown as mean ± SD.

H. VZs number of 03231^p.Q503X and Patient^Corrected organoids. Two-tailed t-test on n = 31 03231^Control and n=25 03231^p.Q503X VZs from 4 independent experiments. Dots represent the mean number of VZs per ROI in individual organoids. P value = 0.0134 . Data shown as mean ± SD.

I. Two-month-old Patient^Correctedorganoids expressing SOX2 and MAP2. Dashed yellow circles identify VZ regions.

J. Two-month-old Patient^p.Q503X organoids with SOX2⁺ and MAP2⁺cells.

K. VZs organization in Patient^Corrected and Patient^p.Q503X organoids. Two-tailed chi-square test on mean values of VZs from 3-9 ROI of 3 organoids, analyzed in 4 independent experiments. P value <0.0001. Data shown as mean ± SD.

L. Two-month-old 03231^Control organoids expressing SOX2 and MAP2 markers.

M. Two-month-old 03231^p.Q503X organoids with SOX2 and MAP2⁺cells.

N. VZs organization in 03231^Control and 03231^p.Q503X organoids. Two-tailed chi-square test on mean values of VZs from 3-9 ROI of 3 organoids, analyzed in 4 independent experiments. P value <0.0001. Data is shown as mean ± SD.

O. Patient^Corrected and Patient^p.Q503X organoids stained for SOX2, NeuN and BrdU.

P. Binning analysis of BrdU⁺/SOX2⁺ cells. Two-way ANOVA performed on 15 Patient ^p.Q503Xventricles and 12 Patient^Corrected from 3 independent experiments. P v alue Bin 1 = 0.4, P v alue Bin 3 = 0.2. Data is shown as mean ± SD.

Q. Binning analysis of BrdU⁺/NeuN⁺ cells. Two-way ANOVA performed on 15 Patient ^p.Q503Xventricles and 12 Patient^Corrected from 3 independent experiments. P v alue Bin 4 = 0.0094. Data represented as mean ± SD.

R. 03231^Control and 03231t^p.Q503X organoids stained SOX2, NeuN and BrdU.

S. Binning analysis of BrdU⁺/SOX2⁺ cells. Two-way ANOVA performed on 18 03231^p.Q503X ventricles and 18 03231^Control ventricles from 3 independent experiments. P v alue Bin 1 = 0.0001>, P v alue Bin 2 = 0.0110, P v alue Bin 3 = 0.0076. Data represented as mean ± SD.

T. Binning analysis of BrdU⁺/NeuN⁺ cells. Two-way ANOVA performed on 18 03231^p.Q503Xventricles and 18 03231^Control ventricles from 3 independent experiments. P v alue Bin 1 = 0.0448, P v alue Bin 3 = 0.0400, P v alue Bin 7 = 0.0094. Data represented as mean ± SD.