Extended Data Table 1. Quantification of protocol efficiency.
Efficiency of dorsal forebrain cell type generation as assessed by IHC for neuronal (MAP2) and dorsal progenitor (PAX6 and EMX1) markers at 1, 3 and 6 months, and by single-cell RNA-seq analysis at 3 and 6 months. In addition to data for the 6 experimental batches described in this study, data for two additional batches, a replicate for the HUES66 and one batch for the additional line Mito 210, are also included in the table. Detailed information about repetitions and efficiency can be found in Methods, in the “Statistics and Reproducibility” section.
| Expression of Neuronal and Cortical Markers by IHC |
Generation of Forebrain Cell Types by RNA-seq |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Timepoint | Cell Line | Batches | Organoids Analyzed | MAP2 | PAX6 | EMX1 | Organoids Analyzed | Reproducibility | ||||
| 1 Mo. | PGP1 | 2 | 7 | 7/7 | 100% | 7/7 | 100% | 7/7 | 100% | |||
| 11a | 1 | 4 | 4/4 | 100% | 4/4 | 100% | 4/4 | 100% | ||||
| GM08330 | 1 | 6 | 6/6 | 100% | 6/6 | 100% | 6/6 | 100% | ||||
| Mito 210 | 1 | 4 | 4/4 | 100% | 4/4 | 100% | 4/4 | 100% | ||||
| HUES66 | 2 | 5 | 5/5 | 100% | 5/5 | 100% | 5/5 | 100% | ||||
| Total | 7 | 26 | 26/26 | 100% | 26/26 | 100% | 26/26 | 100% | ||||
| 3 Mo. | PGP1 | 3 | 10 | 10/10 | 100% | 10/10 | 100% | 9/10 | 90% | 6 (2 batches) | 6/6 | 100% |
| 11a | 1 | 6 | 6/6 | 100% | 6/6 | 100% | 6/6 | 100% | ||||
| GM08330 | 1 | 6 | 6/6 | 100% | 6/6 | 100% | 6/6 | 100% | ||||
| Mito 210 | 1 | 3 | 3/3 | 100% | 3/3 | 100% | 3/3 | 100% | ||||
| HUES66 | 2 | 12 | 12/12 | 100% | 12/12 | 100% | 12/12 | 100% | 3 | 3/3 | 100% | |
| Total | 8 | 37 | 37/37 | 100% | 37/37 | 100% | 36/37 | 97% | 9 | 9/9 | 100% | |
| Mito 210 | 1 | 4 | 4/4 | 100% | 4/4 | 100% | 4/4 | 100% | ||||
| 6 Mo. | PGP1 | 2 | 6 | 6/6 | 100% | 6/6 | 100% | 5/6 | 83% | 6 (2 batches) | 5/6 | 83% |
| 11a | 1 | 3 | 3/3 | 100% | 3/3 | 100% | 3/3 | 100% | 3 | 3/3 | 100% | |
| GM08330 | 1 | 3 | 3/3 | 100% | 3/3 | 100% | 3/3 | 100% | 3 | 3/3 | 100% | |
| HUES66 | 1 | 7 | 7/7 | 100% | 7/7 | 100% | 0/7 | 0% | ||||
| Total | 5 | 19 | 19/19 | 100% | 19/19 | 100% | 11/19 | 58% | 12 | 11/12 | 92% | |
| Total | 8 | 82 | 82/82 | 100% | 82/82 | 100% | 73/82 | 89% | 21 | 20/21 | 95% | |