KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
| ||
| Antibodies | ||
|
| ||
| Anti-Brn2 | Cell Signaling | CAT# 12137S; RRID:AB_2797827 |
| Anti-FoxG1 | Millipore Sigma | CAT# MABD79 |
| Anti-Tuj1 | Aves | CAT# TUJ-0020 |
| Anti-Brn3a | Millipore Sigma | CAT# MAB1585; RRID:AB_94166 |
| Anti-GFAP | Abcam | CAT# ab194324 |
| Anti-S100β | Abcam | CAT# ab52642; RRID:AB_882426 |
| Anti-TDP-43 | Proteintech | CAT# 10782-2-AP; RRID:AB_615042 |
| Anti-Hb9 | DSHB | CAT# 81.5C10; RRID:AB_2145209 |
| Anti-CHAT | EMD millipore | CAT# AB144P-200UL; RRID:AB_2079751 |
| Anti-NeuN | EMD millipore | CAT# ABN78; RRID:AB_10807945 |
| Anti-CHAT 488 | Abcam | CAT# ab192465 |
| Anti-Isl1 568 | Abcam | CAT# ab203406 |
| Anti-pTDP-43 | CosmoBio | CAT# TIP-PTD-M01; RRID:AB_1961900 |
| Anti-GAPDH | Cell Signaling | CAT# 2118S; RRID:AB_561053 |
| Donkey anti-mouse 488 | Thermofisher Scientific | CAT# A21202; RRID:AB_141607 |
| Donkey anti-mouse 568 | Thermofisher Scientific | CAT# A10037; RRID:AB_253401 |
| Donkey anti-rabbit 488 | Thermofisher Scientific | CAT# A21206; RRID:AB_2535792 |
| Donkey anti-goat 555 | Thermofisher Scientific | CAT# A21432; RRID:AB_2535853 |
| Donkey anti-rabbit 568 | Thermofisher Scientific | CAT# A10042; RRID:AB_2534017 |
| Donkey anti-chicken 647 | Jackson Immunoresearch | CAT# 703-605-155; RRID:AB_2340379 |
| Donkey anti-rabbit 647 | Thermofisher Scientific | CAT# A31573; RRID:AB_2536183 |
| IRDye 680RD Goat anti-Mouse IgG | LI-COR | CAT# 926-68070; RRID:AB_10956588 |
| IRDye 800CW Donkey anti-Rabbit IgG | LI-COR | CAT# 926-32213; RRID:AB_621848 |
|
| ||
| Bacterial and virus strains | ||
|
| ||
| NEB 5-alpha Competent E. coli | New England Biolabs | CAT# C2987I |
|
| ||
| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| 16% Formaldehyde | Life Technologies | CAT# 28908 |
| PBS | Gibco | CAT# 10010049 |
| Triton X- | Millipore Sigma | CAT# 9400 |
| Bovine Serum Albumin | Millipore Sigma | CAT# A2153 |
| Hoechst | Thermofisher Scientific | CAT# 62249 |
| Sodium Hydroxide | Sigma-Aldrich | CAT# 72068-100ML |
| Hydrogen Peroxide | Thermofisher Scientific | CAT# H325-500 |
| Cycloheximide | Millipore Sigma | CAT# 01810 |
| Dimethyl Sulfoxide | Sigma | CAT# D2650 |
| Vitronectin XF | Stemcell Technologies | CAT# 07180 |
| mTeSR Plus | Stemcell Technologies | CAT# 100-0275 |
| Accutase | Thermofisher Scientific | CAT# A1110501 |
| Chroman1 | MedChemExpress | CAT# HY-15392 |
| Emricasan | Selleckchem | CAT# S7775 |
| Trans-ISRIB | Tocris | CAT# 5284 |
| Puromycin | InvivoGen | CAT# ant-pr-1 |
| DMEM/F12 | Life Technlologies | CAT# 11320082 |
| N2 supplement | Gibco | CAT# 17502-048 |
| Non-essential amino acids | Corning | CAT# 25-025-CI |
| Glutamax | Thermo | CAT# 35050061 |
| Penicillin/Streptomycin | Life Technlologies | CAT# 15070-063 |
| Doxycycline | Sigma Aldrich | CAT# D9891-1G |
| Compound E | Calbiochem | CAT# 565790-500UG |
| Matrigel | Corning | CAT# 354277 |
| Fetal Bovine Serum | Hyclone | CAT# SH30910.03HI |
| 96-wells plates | Cellvis | CAT# P96-1.5H-N |
| 6-well plates | Corning | CAT# 353046 |
| Polyethylenimene | Sigma | CAT# 03880 |
| Boric Acid | Millipore Sigma | CAT# B6768-500G |
| Sodium Tetraborate | Sigma-Aldrich | CAT# B9876-500G |
| Sodium Chloride | Sigma-Aldrich | CAT# 71376-1KG |
| Laminin | Life Technlologies | CAT# 23017-015 |
| Aphidicolin | Cell Signaling | CAT# 32774 |
| Neurobasal | Life Technologies | CAT# 21103049 |
| Beta mercaptoethanol | Sigma | CAT# M6250-100ML |
| GDNF | Life Technologies | CAT# PHC7044 |
| BDNF | Life Technologies | CAT# PHC7074 |
| CTNF | R&D Systems | CAT# 257-NT-50UG |
| IGF-1 | R&D Systems | CAT# 291-G1-200 |
| Retinoic acid | Sigma | CAT# R2625-50MG |
| B27 supplement | Gibco | CAT# 17504-44 |
| NT-3 | PeproTech | CAT# 450-03 |
| NGF | R&D Systems | CAT# 256-GF |
| Advanced DMEM/F12 | Thermo | CAT# 12634-028 |
| LDN193189 | Stemgent | CAT# 04-0074-02 |
| SB431542 | DNSK | CAT# DNSK-KI-12 |
| Y27632 | Abcam | CAT# ab120129 |
| Astrocyte Media | Sciencell | CAT# 1801 |
| DMEM/F12 | Gibco | CAT# 1132-033 |
| Penicillin/Streptomycin | Gibco | CAT# 15140-122 |
| Fetal Bovine Serum | Sigma | CAT# F0926 |
| Lipofectamine RNAiMAX | Thermofisher Scientific | CAT# 13778075 |
| Opti-MEM | Gibco | CAT# 31985070 |
| QIAshredder | Qiagen | CAT# 79654 |
| KiCqStart SYBR Green | Millipore Sigma | CAT# KCQS00 |
| iTaq | BioRad | CAT# 1725131 |
| RIPA Buffer | Thermofisher Scientific | CAT# 89901 |
| Halt protease and phosphatase inhibitor cocktail | Roche | CAT# 78440 |
| Urea | Millipore Sigma | CAT# U4883-6X25ML |
| Thiourea | Millipore Sigma | CAT# T8656-50G |
| CHAPS | Biotium | CAT# 22024-10g |
| Protease inhibitor cocktail | Roche | CAT# 1873580001 |
| Phosphatase inhibitor cocktail | Sigma | CAT# P5726-5mL |
| NuPAGE LDS sample buffer | Thermofisher Scientific | CAT# NP0007 |
| 4-20% CriterionTM TGXTM Precast Midi 18-well Protein Gel | Bio-Rad | CAT# 5671094 |
| iBlot 2 transfer stacks | Thermofisher Scientific | CAT# IB24001 |
| 1% blocking buffer | Boston BioProducts | CAT# IBB-180X |
|
| ||
| Critical commercial assays | ||
|
| ||
| Human Stem Cell Nucleofector Kit 1 | Lonza | CAT# VPH-5012 |
| RNeasy mini kit | Qiagen | CAT# 74104 |
| High-Capacity cDNA Reverse Transcription Kit | Applied Biosystems | CAT# 4368814 |
| Pierce BCA protein assay kit | Thermofisher Scientific | CAT# 23252 |
|
| ||
| Deposited data | ||
|
| ||
| Bulk RNA-seq from iPSC-derived cells | This paper | dbGAP: phs002440.v2.p1 |
|
| ||
| Experimental models: Cell lines | ||
|
| ||
| CRISPR edited iPSCs | Pereira et al.2 | N/A |
| SH-SY5Y | ATTC | CAT# CRL-2266 |
|
| ||
| Experimental models: Organisms/strains | ||
|
| ||
| NEFH-hTDP-43DNLS transgenic mice | Walker et al.42 | N/A |
|
| ||
| Oligonucleotides | ||
|
| ||
| siRNA against TDP-43 | Dharmacon | CAT# L-012394 |
| siRNA control sequence | Dharmacon | CAT# D001810-10 |
| GAPDH forward: GAAGGTGAAGGTCGGAGTC | This paper | N/A |
| GAPDH reverse: GAAGATGGTGATGGGATTTC | This paper | N/A |
| GAPDH probe: CAAGCTTCCCGTTCTCAGCC | This paper | N/A |
| STMN2 CE forward: CTTTCTCTAGCACGGTCCCAC | This paper | N/A |
| STMN2 CE reverse: ATGCTCACACAGAGAGCCAAATTC | This paper | N/A |
| STMN2 CE probe: CTCTCGAAGGTCTTCTGCCG | This paper | N/A |
| Primers for qRT-PCR, see Table S7 | This paper | N/A |
|
| ||
| Recombinant DNA | ||
|
| ||
| PB-tet-hNIL | This paper | Addgene 197089 |
| PB-tet-NGN2 | This paper | Addgene197090 |
| PB-tet-NB | This paper | Addgene197092 |
| pEIF1 a:Transposase | Michael Ward | Addgene172116 |
|
| ||
| Software and algorithms | ||
|
| ||
| MetaXpress version 6 software | MetaXpress | https://support.moleculardevices.com/ |
| Zen 3.3 software | Zeiss | https://www.zeiss.com/microscopy |
| MATLAB 2018b | MATLAB | https://www.mathworks.com/ |
| STAR (2.7.3a) | Dobin et al.57 | https://github.com/alexdobin/STAR |
| R (4.0.3) | The R Project for Statistical Computing | https://www.r-project.org/ |
| DESeq2 (1.36.0) | Love et al.58 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Integrated Genomics Viewer (2.11.9) | Robinson et al.59 | https://software.broadinstitute.org/software/igv/ |
| SAMtools (1.13) | Danecek et al.60 | http://www.htslib.org/ |
| MAJIQ (2.3) | Green et al.61 | https://majiq.biociphers.org/ |
| BEDtools (2.27.1) | Quinlan etal.62 | https://github.com/arq5x/bedtools2 |
| GOrilla | Eden et al.63 | https://cbl-gorilla.cs.technion.ac.il/ |
| REVIGO | Supek et al.64 | http://revigo.irb.hr/ |
| fgsea (1.22.0) | Subramanian et al.65 | https://github.com/ctlab/fgsea |