Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-histone H2A.X (rabbit IgG, 1:1000) | Abcam | Cat# ab5392 |
| Bungarotoxin (BTX, 1:750) (Alexa594-conjugated) | Invitrogen | Cat# B13423 |
| GFAP (chicken IgY, 1:1000) | Aves Labs Inc | GFAP |
| GR repeat (rabbit IgG, 1:50) | Proteintech | Cat# 23978–1-AP |
| Hb9 (mouse IgG1 kappa light chain, 1:10) | DSHB | Cat# 81.5C10 |
| Iba1 (rabbit IgG, 1:100) | GeneTex | Cat# GT101495 |
| Islet 1 (rabbit IgG, 2 μg/ml) | Abcam | Cat# ab20670 |
| MAP2 (chicken IgY, 1:2000) | Abcam | Cat# ab5392 |
| Mu Crystallin (rabbit IgG, 1: 200) (CoraLite®594-conjugated) | Proteintech | Cat# CL594–12495 |
| Phospho TDP43(Ser409/410) (mouse IgG2a,1:100) | ProteinTech | Cat# 22309–1-AP |
| PR repeat (rabbit IgG, 1:50) | Proteintech | Cat# 23979–1-AP |
| STMN2 (rabbit IgG, 1:200) | Novus | Cat# NBP1–49461 |
| SYF2 (rabbit IgG, 1:80) for iMN staining and western blots | MilliporeSigma | Cat# HPA070710 |
| SYF2 (mouse IgG, 1:150) for post-mortem tissue staining | Abcam | Cat# ab236417 |
| Synaptophysin (rabbit IgG, 1:100) | Synaptic systems | Cat# 101002 |
| TDP43 (rabbit IgG, 1:200) | Proteintech | Cat# 10782–2-AP |
| Tuj1 (mouse IgG, 1:1000) | Biolegend | Cat# 801202 |
| DAPI | Thermo Fisher Scientific | Cat# 62248 |
| Donkey Anti-Chicken IgY (IgG) (H+L) Alexa Fluor® 647 | Jackson ImmunoResearch | Cat# 703–605-155 |
| Donkey anti-Mouse, IgG (H+L) Highly Cross-Adsorbed, Alexa Fluor® 488 | Invitrogen | Cat# A21202 |
| Donkey anti-Mouse, IgG (H+L) Highly Cross-Adsorbed, Alexa Fluor® 555 | Invitrogen | Cat# A31570 |
| Donkey anti-Mouse, IgG (H+L) Highly Cross-Adsorbed, Alexa Fluor® 647 | Invitrogen | Cat# A32787 |
| Donkey anti-Rabbit, IgG (H+L) Highly Cross-Adsorbed, Alexa Fluor® 488 | Invitrogen | Cat# A-21206 |
| IRDye® 680RD Donkey anti-Rabbit IgG Secondary Antibody | LI-COR Biosciences | Cat# 926–68073 |
| IRDye® 800CW Donkey anti-Mouse IgG Secondary Antibody | LI-COR Biosciences | Cat# 926–32212 |
| NeuroTrace™ 500/525 Green Fluorescent Nissl Stain (1:50) | Thermo Fisher Scientific | Cat# N21480 |
| Biological samples | ||
| CTRL (1) | Johns Hopkins ALS Postmortem Resource Core | JHU124 |
| CTRL (2) | Johns Hopkins ALS Postmortem Resource Core | JHU129 |
| CTRL (3) | BioChain Institute Inc. | T2234234 |
| sALS (1) | Johns Hopkins ALS Postmortem Resource Core | JHU121 |
| sALS (2) | Johns Hopkins ALS Postmortem Resource Core | JHU122 |
| sALS (3) | Johns Hopkins ALS Postmortem Resource Core | JHU126 |
| sALS (4) | Johns Hopkins ALS Postmortem Resource Core | JHU127 |
| sALS (5) | Johns Hopkins ALS Postmortem Resource Core | JHU128 |
| Chemicals, peptides, and recombinant proteins | ||
| DMEM | Gibco | Cat# 11995–065 |
| Opti-MEM | Gibco | Cat# 31985–070 |
| FBS | GenClone | Cat# 25–514 |
| Trypsin | GenClone | Cat# 25–510 |
| Polybrene (Hexadimethrine bromide) | Millipore Sigma | Cat# H9268–5G |
| DMEM/F12 | Corning | Cat# 10–090-CV |
| Laminin | Invitrogen | Cat#23017015 |
| Glutamax | Gibco | Cat# 35050–061 |
| N2 supplement | Gibco | Cat# 17502048 |
| B27 supplement | Gibco | Cat# 17504044 |
| Non-essential amino acids (NEAA) | Gibco | Cat# 11140050 |
| Human FGF-beta | Peprotech | Cat# 100–18B |
| Repsox | Selleckchem | Cat# S7223 |
| human CNTF | R&D | Cat# 257-NT |
| human BDNF | R&D | Cat# 248BDB |
| human GDNF | R&D | Cat# 212-GD |
| Alt-R® S.p. HiFi Cas9 Nuclease V3, (100 μg) | IDT | Cat# 1081060 |
| Matrigel | Corning | Cat#3 54277 |
| mTeSR | StemCell | Cat# 85851 |
| Accutase | Innovative Cell Technologies | Cat# AT4104 |
| Y-27632 2HCl (ROCK inhibitor) | Selleckchem | Cat# S1049 |
| Lenti-X concentrator | TaKaRa | Cat# 631232 |
| Polybrene (Hexadimethrine bromide) | Millipore Sigma | Cat# H9268–5G |
| Neurobasal-A | Life Technologies | Cat# 10888–022 |
| Apilimod | achemblock | Cat# O33822 |
| SB431542 | Cayman Chemical | Cat# 13031 |
| CHIR99021 | Cayman Chemical | Cat# 13122 |
| Retinoic Acid | Millipore Sigma | Cat# R2625 |
| DMH1 | Selleckchem | Cat# S7146 |
| Purmorphamine | Cayman Chemical | Cat# 10009634 |
| T-PER buffer | Thermofisher | Cat# 78510 |
| Donor Equine Serum | HyClone | Cat# 16777–030 |
| MEM media | Life Technologies | Cat# 10370088 |
| Penicillin-streptomycin 50X | Corning | Cat# 30–001-CI |
| Compound E | Cayman Chemicals | Cat# 15579 |
| Digitonin | Cayman Chemicals | Cat# 14952 |
| 5-Ethynyl uridine | Millipore Sigma | Cat# 909475 |
| Blasticidin S HCl | ThermoFisher | Cat# A1113903 |
| Lipofectamine™ Stem Transfection Reagent | Thermo | Cat# STEM00001 |
| Doxycycline | Clontech | Cat# 631311 |
| BrdU | Millipore Sigma | Cat# B9285 |
| Puromycin | Millipore Sigma | Cat# SBR00017 |
| Spectrum Collection | Microsource Discovery Systems | The Spectrum collection |
| Doramectin | Microsource Spectrum | Cat# 01505902 |
| Avermectin A1a | Microsource Spectrum | Cat# 01502347 |
| Abamectin (avermectin B1a) | Cayman Chemical | Cat# 19201 |
| Moxidectin | Cayman Chemical | Cat# 17165 |
| Selamectin | Cayman Chemical | Cat# 21529 |
| Eprinomectin | Millipore Sigma | Cat# 32526 |
| Ivermectin | Selleckchem | Cat# S1351 |
| Cloxyquin (5 chloro-8-quinolinol) 95% | Millipore Sigma | Cat# C47000 |
| Dicloxacillin sodium | Millipore Sigma | Cat# D9016 |
| Ibuprofen | Millipore Sigma | Cat# I4883 |
| Acetylcholine chloride | Tocris Bioscience | Cat# 2809 |
| Salsolidine | abCam | Cat# ab143546 |
| Alfuzosin hydrochloride | Cayman Chemicals | Cat# 13648 |
| Canrenone | Cayman Chemicals | Cat# 21307 |
| Torsemide | Selleckchem | Cat# S1698 |
| Phenazopyridine hydrochloride | Millipore Sigma | Cat# 34076 |
| Phenelzine sulfate | Millipore Sigma | Cat# P6777 |
| Levonorgestrel | Cayman Chemicals | Cat# 10006318 |
| Dexibuprofen | Cayman Chemicals | Cat# 16793 |
| Amlexanox | Cayman Chemicals | Cat# 14181 |
| Deflazacort | Cayman Chemicals | Cat# 20386 |
| Levetiracetam | Tocris Bioscience | Cat# 2839 |
| Alpha tocopherol | Millipore Sigma | Cat# 258024 |
| Alpha tocopheryl acetate | Cayman Chemicals | Cat# 10007705 |
| Capecitabine | Cayman Chemicals | Cat# 10487 |
| Anastrozole | Millipore Sigma | Cat# A2736 |
| Fulvestrant | Cayman Chemicals | Cat# 10011269 |
| Lomustine | Millipore Sigma | Cat# L5918 |
| Pemetrexed | Cayman Chemicals | Cat# 14269 |
| Acenocoumarol | Cayman Chemicals | Cat# 10010569 |
| Clinafloxacin Hydrochloride | Cayman Chemicals | Cat# 16923 |
| CoEnzyme Q10 (Ubidecarenone) | Selleckchem | Cat# S2398 |
| Pirenzepine hydrochloride | Tocris Bioscience | Cat# 1071 |
| Ketoprofen | Cayman Chemicals | Cat# 10006661 |
| Cefsulodin | Cayman Chemicals | Cat# 16127 |
| Cefoperazone | Cayman Chemicals | Cat# 16113 |
| Cycloheximide | Cayman Chemicals | Cat# 14126 |
| Menadione | Cayman Chemicals | Cat# 15950 |
| β-carotene | Cayman Chemicals | Cat# 16837 |
| Pyrazinamide | Cayman Chemicals | Cat# 23416 |
| Salicyclic Acid | Selleckchem | Cat# S4539 |
| Sulfabenzamide | Selleckchem | Cat# S4576 |
| Sulfacetamide | Cayman Chemicals | Cat# 20377 |
| Tetracycline hydrochloride | Cayman Chemicals | Cat# 14328 |
| Thioguanine | Cayman Chemicals | Cat# 15774 |
| Timolol maleate | Selleckchem | Cat# S4123 |
| Tolmetin sodium | Cayman Chemicals | Cat# 18195 |
| Ursodiol | Selleckchem | Cat# S1643 |
| Azlocillin sodium | Cayman Chemicals | Cat# 18424 |
| Cefaclor | Santa Cruz Biotechnology | Cat# sc-205242 |
| Vidarabine | Cayman Chemicals | Cat# 18149 |
| Arecoline | Cayman Chemicals | Cat# 13662 |
| Mebeverine hydrochloride | Santa Cruz Biotechnology | Cat# sc-235579 |
| Paromomycin sulfate | Cayman Chemicals | Cat# 23634 |
| Cytisine | Selleckchem | Cat# S2287 |
| Ftaxilide | Microsource Spectrum | Cat# 01504523 |
| Bambuterol hydrochloride | Selleckchem | Cat# S4277 |
| Bucladesine | Selleckchem | Cat# S7858 |
| Hexamethonium bromide | Selleckchem | Cat# S4069 |
| Niacin | Selleckchem | Cat# S1744 |
| Nifedipine | Cayman Chemicals | Cat# 11106 |
| Norethynodrel | Microsource Spectrum | Cat# 01500435 |
| Norgestrel | Cayman Chemicals | Cat# 10006319 |
| Noscapine hydrochloride | Cayman Chemicals | Cat# 17255 |
| Phenacemide | Microsource Spectrum | Cat# 01500472 |
| Pheniramine maleate | Selleckchem | Cat# S4045 |
| Phenylbutazone | Cayman Chemicals | Cat# 70400 |
| Levosimendan | Cayman Chemicals | Cat# 16128 |
| Nortriptyline hydrochloride | Cayman Chemicals | Cat# 15904 |
| Oxidopamine hydrochloride | Microsource Spectrum | Cat# 01500450 |
| Tibolone | Cayman Chemicals | Cat# 10006321 |
| Exemestane | Cayman Chemicals | Cat# 15008 |
| Metformin | Selleckchem | Cat# S1950 |
| Ganciclovir | Cayman Chemicals | Cat# 13853 |
| Letrozole | Cayman Chemicals | Cat# 11568 |
| Dihydrotestosterone | Cayman Chemicals | Cat# 15874 |
| Riluzole | Millipore Sigma | Cat# R116 |
| Edaravone | Selleckchem | Cat# S1326 |
| Fluphenazine | Cayman Chemicals | Cat# 23555 |
| Critical commercial assays | ||
| Click-iT RNA Alexa Fluor 594 imaging kit | Thermo Fisher Scientific | Cat# C10330 |
| RNeasy 96 kit | Qiagen | Cat# 74181 |
| RNeasy plus mini kit | Qiagen | Cat# 74136 |
| Pierce™ BCA Protein assay kit | Thermo Fisher Scientific | Cat# 23227 |
| Deposited data | ||
| Sequence Read Archive (SRA) (Whole exome sequencing of sALS patients) | https://www.ncbi.nlm.nih.gov/sra | PRJNA552114 |
| Sequence Read Archive (SRA) (Whole exome sequencing of sALS patients) | https://www.ncbi.nlm.nih.gov/sra | PRJNA903195 |
| Gene Expression Omnibus (Bulk RNA-seq and splicing analysis) | https://www.ncbi.nlm.nih.gov/geo/ | GSE218079 |
| Experimental models: Cell lines | ||
| CTRL-1 | NINDS Biorepository | ND03231 |
| CTRL-2 | NINDS Biorepository | ND03719 |
| CTRL-3 | NINDS Biorepository | ND05280 |
| CTRL-4 | NINDS Biorepository | ND00184 |
| CTRL-5 | NINDS Biorepository | ND41865 |
| CTRL-6 | Cedars Sinai Biomanufacturing Center | CS5MRLiCTR |
| CTRL-7 | Cedars Sinai Biomanufacturing Center | CS2PFYiCTR |
| CTRL-8 | Cedars Sinai Biomanufacturing Center | CS2BVGiCTR |
| CTRL-9 | Cedars Sinai Biomanufacturing Center | CS2GW3iCTR |
| C9-ALS/FTD-1 | NINDS Biorepository | ND06769 |
| C9-ALS/FTD-2 | NINDS Biorepository | ND10689 |
| C9-ALS/FTD-3 | NINDS Biorepository | ND12099 |
| C9-ALS/FTD-4 | Cedars Sinai Biomanufacturing Center | CS29iALS |
| C9-ALS/FTD-5 | Cedars Sinai Biomanufacturing Center | CS2YNLiALS |
| C9-ALS/FTD-6 | NINDS Biorepository | ND08957 |
| C9-ALS/FTD-7 | NINDS Biorepository | ND12100 |
| C9-ALS/FTD-8 | Cedars Sinai Biomanufacturing Center | CS2DDGiALS |
| C9-ALS/FTD-9 | NINDS Biorepository | ND50000 |
| C9-ISO-1 | Ichida Lab | 6769 iso c1 |
| C9-ISO-4 | Cedars Sinai Biomanufacturing Center | 29iALS-ISO |
| sALS-1 | NINDS Biorepository | ND08705 |
| sALS-2 | NINDS Biorepository | ND09292 |
| sALS-3 | NINDS Biorepository | ND09329 |
| sALS-4 | NINDS Biorepository | ND10739 |
| sALS-5 | NINDS Biorepository | ND13454 |
| sALS-6 | NINDS Biorepository | ND14185 |
| sALS-7 | Loma Linda University | #3 |
| sALS-8 | Loma Linda University | #4 |
| sALS-9 | NINDS Biorepository | ND09711 |
| sALS-10 | NINDS Biorepository | ND11813 |
| sALS-11 | NINDS Biorepository | ND50073 |
| sALS-12 | Cedars Sinai Biomanufacturing Center | CS0WD8iALS |
| sALS-13 | Cedars Sinai Biomanufacturing Center | CS0KHAiALS |
| sALS-14 | Ichida Lab | sALS-14 |
| sALS-15 | Cedars Sinai Biomanufacturing Center | CS0GR5iALS |
| sALS-16 | Acurastem Inc | ALS93E |
| sALS-17 | Cedars Sinai Biomanufacturing Center | CS3XLKiALS |
| sALS-18 | Cedars Sinai Biomanufacturing Center | CS2NDDiALS |
| sALS-19 | Cedars Sinai Biomanufacturing Center | CS2WW0iALS |
| sALS-20 | Cedars Sinai Biomanufacturing Center | CS1RUGiALS |
| sALS-21 | Cedars Sinai Biomanufacturing Center | CS2CLNiALS |
| sALS-22 | NINDS Biorepository | ND50082 |
| sALS-23 | Cedars Sinai Biomanufacturing Center | CS2VU4iALS |
| sALS-24 | Cedars Sinai Biomanufacturing Center | CS5HF7iALS |
| sALS-25 | Cedars Sinai Biomanufacturing Center | CS0KBHiALS |
| sALS-26 | Cedars Sinai Biomanufacturing Center | CS3AH9iALS |
| sALS-27 | Cedars Sinai Biomanufacturing Center | CS0JCLiALS |
| TARDBP-ALS/FTD-1 | NINDS Biorepository | ND50007 |
| TARDBP-ALS/FTD-2 | Grupo de Neurociencias de Antioquia - Universidad de Antioquia | 12240 |
| FUS-ALS-1 | NINDS Biorepository | ND35663 |
| FUS-ALS-2 | NINDS Biorepository | ND39034 |
| SOD1-ALS-1 | NINDS Biorepository | ND35658 |
| SOD1-ALS-2 | NINDS Biorepository | ND35659 |
| SOD1-ALS-3 | Kiskinis Lab | 39B |
| CMT2A-1 | New York Stem Cell Foundation | NYCSF-AG0017–01-MR |
| MAPT-1 | Tau consortium | ND32951A.15ᐃ2B09 |
| Experimental models: Organisms/strains | ||
| Mice: Tg(Thy1-TARDBP)4Singh | The Jackson Laboratory | Strain# 012836 |
| Mice: C57BL/6J mice | The Jackson Laboratory | Strain# 000664 |
| Mice: ICR/Ha J mice | The Jackson Laboratory | Strain# 009122 |
| Oligonucleotides | ||
| sgRNA-1 targeting upstream of repeat expansion | This paper | GUAACCUACGGUGUCCCGCU |
| sgRNA-2b targeting downstream of repeat expansion | This paper | ACCCCAAACAGCCACCCGCC |
| Primer 1 for repeat primed PCR | This paper | FAM-tgtaaaacgacggccagtCAAGGAGGGAAACAACCGCAGCC |
| Primer 2 for repeat primed PCR | This paper | caggaaacagctatgaccGGGCCCGCCCCGACCACGCCCCGGCCCCGGCCCCGG |
| Primer 3 for repeat primed PCR | This paper | caggaaacagctatgacc |
| CLYBL crRNA | Synthego | ATGTTGGAAGGATGAGGAAA |
| qPCR primer for HPRT, Forward | This paper | GACTTTGCTTTCCTTGGTCAG |
| qPCR primer for HPRT, Reverse | This paper | GGCTTATATCCAACACTTCGTGGG |
| qPCR primer for SYF1, Forward | This paper | CATTTCGAGAAGGCTCGGGA |
| qPCR primer for SYF1, Reverse | This paper | CAGCTGTCCGTTGTCCTCAT |
| Software and algorithms | ||
| Image J | https://imagej.nih.gov/ij/ | N/A |
| Prism | https://www.graphpad.com/scientific-software/prism/ | N/A |
| Next-generation clustered heat map builder and viewer | https://bioinformatics.mdanderson.org/public-software/ngchm/ | N/A |
| R studio | https://www.rstudio.com/ | N/A |
| Biorender | https://biorender.com/ | N/A |