KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| ALDH1L1 (mouse monoclonal IgG3) | Abcam | ab56777; RRID:AB_940204 |
| AT8 (mouse monoclonal IgG1) | Invitrogen | MN1020: RRID:AB_223647 |
| β-tubulin III (mouse monoclonal IgG2b) | Sigma | T-8660; RRID:AB_477590 |
| BRN2 (mouse monoclonal IgG1) | Millipore | MAB-D51; RRID:AB_11204531 |
| Calbindin 1(rabbit) | Swant | cb-38a |
| Cathepsin D (rabbit polyclonal) | Gift from Dr. Stuart Kornfeld lab | RRID:AB_2314096 |
| CTIP2 (rat monoclonal IgG2a) | Abcam | ab18465; RRID:AB_2064130 |
| ELAVL4 (HuD-E1) (mouse IgG2a) | SantaCruz | sc-28299; RRID:AB_627765 |
| FOXG1 (rabbit polyclonal) | Takara | M227; RRID:ZFIN_ZDB-ALT-980203-55 |
| G3BP (mouse monoclonal IgG1) | BD Biosciences | 611126; RRID:AB_398437 |
| G3BP1 (rabbit polyclonal) | Protein Tech | 13057-2-AP; RRID:AB_2232034 |
| GAPDH (rabbit monoclonal) | Cell Signaling Technology | 2118S; RRID:AB_561053 |
| GFAP (mouse monoclonal IgG1) | Millipore | MAB3402; RRID:AB_94844 |
| GFAP, clone EP672Y (rabbit) | Ventana | 760-4345 |
| Homer1 (mouse monoclonal IgG1) | SYSY | 160011; RRID:AB_2795016 |
| Iba1 (rabbit polyclonal) | Invitrogen | PA5-27436; RRID:AB_2544912 |
| Ki67 (rat monoclonal IgG2a) | Thermo Fisher | 14-5698-82; RRID:AB_10854564 |
| LAMP1 (rabbit polyclonal) | Abcam | 24170; RRID:IMSR_CMMR:PST24170 |
| LC3I/II (rabbit polyclonal) | Novus Biologicals | NB100-2331; RRID:IMSR_CMMR:PST24170 |
| MAP2 (chicken) | Aves labs | MAP; RRID:AB_2313549 |
| MAP2 (rabbit polyclonal) | Abcam | ab32454; RRID:AB_776174 |
| MAP2ab (chicken polyclonal) | Abcam | ab5392; RRID:AB_2138153 |
| MEF2C (rabbit polyclonal) | Novus | NBP2-17260 |
| Nestin (mouse monoclonal IgG1) | Millipore | MAB5326; RRID:AB_11211837 |
| NeuN (mouse monoclonal IgG1) | Millipore | MAB377; RRID:AB_2298767 |
| NeuN (mouse monoclonal IgG2b) | Abcam | 104224; RRID:Addgene_104224 |
| NeuN (rabbit monoclonal) | Abcam | Ab177487; RRID:AB_2532109 |
| p62 (mouse monoclonal) | Abnova | H00008878-M01; RRID:AB_437085 |
| p62 Ick ligand (mouse monoclonal) | BD Transductions | 610832; RRID:AB_398151 |
| PAX6 (rabbit polyclonal) | BioLegend | 901301; RRID:AB_2565003 |
| PHF-1 (mouse IgG1) | Gift from Dr. Peter Davies | N/A |
| Phospho-Tau Ser396 (rabbit polyclonal) | Thermo Fisher | 44752G; RRID:AB_2533745 |
| S100beta (rabbit polyclonal) | DAKO Potts | Z0311; RRID:AB_10013383 |
| SATB2 (mouse monoclonal IgG1) | Abcam | ab51502; RRID:AB_882455 |
| SOX10 (A-2) (mouse monoclonal IgG1) | Santa Cruz | sc-365692; RRID:AB_10844002 |
| SOX2 (E4) (mouse monoclonal IgG1) | Santa Cruz | sc-365823; RRID:AB_10842165 |
| Synapsin1 (rabbit polyclonal) | Millipore | AB1543; RRID:AB_2200400 |
| TAU (4 Repeat Isoform RD4) (mouse monoclonal IgG) | EMD Millipore | 05-804; RRID:AB_310014 |
| TBR1 (rabbit polyclonal) | Abcam | ab31940; RRID:AB_2200219 |
| TIA1 (mouse monoclonal IgG1) | SantaCruz | sc-166247; RRID:AB_2201545 |
| Total TAU (rabbit polyclonal) | DAKO Potts | A-0024; RRID:AB_10013724 |
| Total TAU DA9 (mouse IgG1) | Gift from Peter Davies | N/A |
| Total TAU, HT7 (mouse monoclonal IgG1) | Thermo Fisher | MN1000; RRID:AB_2314654 |
| Total TAU, TAU5 (mouse monoclonal IgG1) | Thermo Fisher | AHB0042; RRID:AB_1502093 |
| Ubiquitin (rabbit polyclonal) | Cell Signaling Technology | 3933S; RRID:AB_2180538 |
| VGLUT1 (guinea pig) | Gift from Susan Morton, Tom Jessell | N/A |
| Goat anti-chicken IgG-Alexa 647 | Invitrogen | A-21449; RRID:AB_2535866 |
| Goat anti-guinea pig-Alexa 647 | Jackson | 106-605-003; RRID:AB_2337446 |
| Goat anti-guinea pig-Cy3 | Jackson | 106-165-003; RRID:AB_2337423 |
| Goat anti-mouse HRP linked | Cell Signaling Technology | 7076s; RRID:AB_330924 |
| Goat anti-mouse IgG1-Alexa 488 | Invitrogen | A-21121; RRID:AB_2535764 |
| Goat anti-mouse IgG1-Alexa 546 | Invitrogen | A-21123; RRID:AB_141592 |
| Goat anti-mouse IgG1-Alexa 647 | Invitrogen | A-21240; RRID:AB_141658 |
| Goat anti-mouse IgG2a-Alexa 488 | Invitrogen | A-21131; RRID:AB_141618 |
| Goat anti-mouse IgG2b-Alexa 546 | Invitrogen | A21143; RRID:AB_1500891 |
| Goat anti-rabbit HRP linked | Cell Signaling Technology | 7074s; RRID:AB_2099233 |
| Goat anti-rabbit-Alexa 488 | Jackson | 111-545-144; RRID:AB_2338052 |
| Goat anti-rabbit-Alexa 647 | Jackson | 111-605-144; RRID:AB_2338078 |
| Goat anti-rabbit-Cy3 | Jackson | 111-165-045; RRID:AB_2338003 |
| OptiView DAB IHC Detection Kit | Roche | 760-700; RRID:AB_2833075 |
| ultraView Universal DAB Detection Kit | Roche | 760-500; RRID:AB_2753116 |
| Chemicals, peptides, and recombinant proteins | ||
| DMEM/F12 | Corning | 10-090-CV |
| Essential 6 medium (E6) | Life Technologies | A1516401 |
| Essential 8 medium (E8) | Life Technologies | A1517001 |
| mTeSR1 medium | StemCell Technologies | 85850 |
| Neurobasal-A ([−] L-glutamine) | Life Technologies | 10888-022 |
| Accutase | StemCell Technologies | 7922 |
| Antibiotic-Antimycotic (Anti-A) 100X | Life Technologies | 15240-062 |
| B-27 supplement without vitamin A | Life Technologies | 12587010 |
| Dispase | StemCell Technologies | 07923 |
| GlutaMAX Supplement | Life Technologies | 3505-061 |
| KnockOut Serum Replacement | Thermo | 10828028 |
| Matrigel | Corning | 356231 |
| Anti-Adherence Rinsing Solution | StemCell Technologies | 07010 |
| MEM Non-essential amino acids 100X | Thermo | 11140050 |
| Penicillin-streptomycin 50X | Corning | 30-001-CI |
| (+)-MK-801 (hydrogen maleate) | Cayman | 10009019 |
| Apilimod | AChemBlock | O33822 |
| CNQX | Cayman | 14618 |
| Dorsomorphin | Tocris | 3093 |
| Dorsomorphin | Cayman | 11967 |
| L-Glutamic acid monosodium salt hydrate | Millipore | G1626 |
| Nimodipine | Cayman | 14573 |
| SB-431542 | Tocris | 1614 |
| SB-431542 | Cayman | 13031 |
| XAV-939 | Tocris | 3748 |
| Y-27632 | Tocris | 1254 |
| β-mercaptoethanol | Sigma | M6250 |
| human BDNF | Peprotech | 450-02 |
| human BDNF | R&D | 248-BDB |
| human EGF | Peprotech | AF-100-15 |
| human NT3 | Peprotech | 450-03 |
| rhFGF2 | R & D systems | 233-FB |
| rhFGF2 | Peprotech | 100-18B |
| Protease Inhibitor cocktail | Sigma | P2714 |
| Deposited data | ||
| Bulk RNA-seq data from 2-, 4- and 6-month organoids | GEO: GSE171345 | |
| Single-cell RNA-seq data from 2-, 4- and 6-month organoids | GEO: GSE171345 | |
| Experimental models: Cell lines | ||
| ND32951A.15Δ1B06 (V337V) | Tau Consortium | ND-B06 |
| ND32951A.15Δ2B09 (V337M) | Tau Consortium | ND-B09 |
| GIH-6-C1-ΔA02 (V337M) | Tau Consortium | GIH6-A02 |
| GIH-6-C1Δ1E11 (V337V) | Tau Consortium | GIH6-E11 |
| GIH-7-C2-Δ2A01 (V337M) | Tau Consortium | GIH7-A01 |
| GIH-7-C2-Δ2B12 (V337V) | Tau Consortium | GIH7-B12 |
| GIH-7-C2-Δ2F02 (V337V) | Tau Consortium | GIH7-F02 |
| ND03231 (Population Control) | NINDS Biorepository | 3231 |
| Software and algorithms | ||
| QuPath | Bankhead et al. (2017) | https://qupath.github.io/ |
| Seurat 3.0 (dev) | Stuart et al. (2019); Butler et al. (2018) | https://satijalab.org/seurat/ |
| Monocle3 | Trapnell et al. (2014); Qiu et al. (2017) | https://cole-trapnell-lab.github.io/monocle3/ |
| SingleR | Aran et al. (2019) | https://bioconductor.org/packages/devel/bioc/vignettes/SingleR/inst/doc/SingleR.html |
| Script for differential gene expression over pseudotime trajectories | Kanton et al. (2019) | N/A |
| ImageJ | https://imagej.nih.gov/ij/index.html | |
| Other | ||
| GW17-18 cortical scRNA-seq data | Polioudakis et al. (2019) | http://solo.bmap.ucla.edu/shiny/webapp/ |
| Adult astrocyte bulk RNaseq data | Zhang et al. (2016) | https://www.brainrnaseq.org/ |
| ELAVL RIP-seq data | Scheckel et al. (2016) | N/A |