KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit Anti-Nup50 | Abcam | Cat#ab137092 |
| Rabbit Anti-Nup153 | Abcam | Cat#ab84872; RRID: AB_1859766 |
| Mouse Anti-TPR | Santa Cruz Biotechnology | Cat#sc-271565; RRID: AB_10649043 |
| Rabbit Anti-Nup54 | Abcam | Cat#ab220890 |
| Mouse Anti-NUPL1 | Abcam | Cat#ab69954; RRID: AB_1269611 |
| Rat Anti-Nup62 | Millipore | Cat#MABE1043 |
| Rat Anti-Nup98 | Abcam | Cat#ab50610; RRID: AB_881769 |
| Rabbit Anti-GP210 | Abcam | Cat#ab15601; RRID: AB_2236461 |
| Rabbit Anti-TMEM48 | Thermo Fisher Scientific | Cat#PA5-67130; RRID: AB_2664610 |
| Rabbit Anti-TMEM48 | Novus Biologicals | Cat#NBP1-91604; RRID: AB_11042869 |
| Rabbit Anti-TMEM48 | Novus Biologicals | Cat#NBP1-91603; RRID: AB_11030742 |
| Rabbit Anti-POM121 | Thermo Fisher Scientific | Cat#PA5-36498; RRID: AB_2553555 |
| Rabbit Anti-POM121 | Novus Biologicals | Cat#NBP2-19890 |
| Mouse Anti-Nup93 | Santa Cruz Biotechnology | Cat#sc-374399; RRID: AB_10990113 |
| Rabbit Anti-Nup155 | Abcam | Cat#ab199528 |
| Rabbit Anti-Nup188 | Thermo Fisher Scientific | Cat#PA5-63984; RRID: AB_2644894 |
| Mouse Anti-Nup205 | Santa Cruz Biotechnology | Cat#sc-377047 |
| Rabbit Anti-AHCTF1 | Thermo Fisher Scientific | Cat#PA5-56812; RRID: AB_2637780 |
| Rabbit Anti-Nup37 | Thermo Fisher Scientific | Cat#PA5-66007; RRID: AB_2664134 |
| Rabbit Anti-Nup43 | Abcam | Cat#ab69447; RRID: AB_1269608 |
| Mouse Anti-Nup107 | Thermo Fisher Scientific | Cat#MA110031; RRID: AB_2154446 |
| Mouse Anti-Nup133 | Santa Cruz Biotechnology | Cat#sc-376699; RRID: AB_11149388 |
| Rabbit Anti-Nup133 | Abcam | Cat#ab155990 |
| Rabbit Anti-Nup160 | Abcam | Cat#ab74147; RRID: AB_1524055 |
| Rabbit Anti-Nup88 | Abcam | Cat#ab79785; RRID: AB_2042496 |
| Rabbit Anti-Nup214 | Bethyl Laboratories | Cat#A300-716A; RRID: AB_533409 |
| Mouse Anti-RANBP2 | Santa Cruz Biotechnology | Cat#sc-74518; RRID: AB_2176784 |
| Mouse Anti-414 | Abcam | Cat#ab50008; RRID: AB_881761 |
| Chicken Anti-NeuN | Millipore | Cat#ABN91; RRID: AB_11205760 |
| Chicken Anti-GFP | Millipore | Cat#AB16901; RRID: AB_90890 |
| Mouse Anti-TurboGFP | Origene Technologies | Cat#TA150041; RRID: AB_2622256 |
| Rabbit Anti-TurboGFP | Thermo Fisher Scientific | Cat#PA5-22688; RRID: AB_2540616 |
| Rabbit Anti-TDP-43 | ProteinTech | Cat#10782-2-AP; RRID: AB_615042 |
| Guinea Pig Anti-Map2 | Synaptic Systems | Cat#188004; RRID: AB_2138181 |
| Mouse Anti-Ran | BD Biosciences | Cat#610341; RRID: AB_397731 |
| Mouse Anti-SMI32 | Covance | Cat#SMI-32P; RRID: AB_2314912 |
| Mouse Anti-Tuj1 | Sigma Aldrich | Cat#MAB1637; RRID: AB_2210524 |
| Rat Anti-NKX6.1 | DSHB | Cat#F55A12; RRID: AB_532379 |
| Goat Anti-Islet1 | R&D Systems | Cat#AF1837; RRID: AB_2126324 |
| Goat Anti-Olig2 | R&D Systems | Cat#AF2418; RRID: AB_2157554 |
| Rabbit Anti-C9ORF72 | ProteinTech | Cat#22637-1-AP; RRID: AB_10953528 |
| Mouse Anti-GAPDH | Life Technologies | Cat#AM4300; RRID: AB_2536381 |
| Rabbit Anti-Alpha Tubulin | Cell Signaling | Cat#2125; RRID: AB_2619646 |
| Mouse Anti-DIG | Jackson Immunoresearch | Cat#200-002-156; RRID: AB_2339005 |
| Goat Anti-Mouse Alexa 488 | Invitrogen | Cat#A11029; RRID: AB_138404 |
| Goat Anti-Rabbit Alexa 488 | Invitrogen | Cat#A11034; RRID: AB_2576217 |
| Goat Anti-Rat Alexa 488 | Invitrogen | Cat#A11006; RRID: AB_2534074 |
| Goat Anti-Chicken Alexa 488 | Invitrogen | Cat#A11039; RRID: AB_142924 |
| Goat Anti-Mouse Alexa 568 | Invitrogen | Cat#A11031; RRID: AB_144696 |
| Goat Anti-Rabbit Alexa 568 | Invitrogen | Cat#A11036; RRID: AB_143011 |
| Goat Anti-Rat Alexa 568 | Invitrogen | Cat#A11077; RRID: AB_141874 |
| Goat Anti-Guinea Pig Alexa 568 | Invitrogen | Cat#A11075; RRID: AB_141954 |
| Goat Anti-Mouse Alexa 647 | Invitrogen | Cat#A21236; RRID: AB_141725 |
| Goat Anti-Rabbit Alexa 647 | Invitrogen | Cat#A21245; RRID: AB_141775 |
| Goat Anti-Rat Alexa 647 | Invitrogen | Cat#A21247; RRID: AB_141778 |
| Goat Anti-Chicken Alexa 647 | Invitrogen | Cat#A21449; RRID: AB_1500594 |
| Goat Anti-Guinea Pig Alexa 647 | Invitrogen | Cat#A21450; RRID: AB_141882 |
| Donkey Anti-Mouse Alexa 488 | Invitrogen | Cat#A21202; RRID: AB_141607 |
| Donkey Anti-Rat Alexa 488 | Invitrogen | Cat#A21208; RRID: AB_141709 |
| Donkey Anti-Mouse Alexa 568 | Invitrogen | Cat#A10037; RRID: AB_2534013 |
| Donkey Anti-Goat Alexa 568 | Invitrogen | Cat#A11057; RRID: AB_142581 |
| Donkey Anti-Rabbit IgG HRP | Thermo Fisher Scientific | Cat#45-000-682 |
| Horse Anti-Mouse IgG HRP | Cell Signaling | Cat#7076S; RRID: AB_330924 |
| Mouse IgG Isotype Control | Thermo Fisher Scientific | Cat#02-610-0; RRID: AB_2532935 |
| Rabbit IgG Isotype Control | Thermo Fisher Scientific | Cat#02-610-2; RRID: AB_2532938 |
| Biological Samples | ||
| Non-neurological control and C9orf72 postmortem tissue | Target ALS Human Postmortem Tissue Core | N/A |
| C9orf72 postmortem tissue | Emory University ADRC Tissue Bank | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| LDN193189 | Stemgent | Cat#04-0074-02 |
| SB431542 | STEMCELL Technologies | Cat#72234 |
| CHIR99021 | Sigma-Aldrich | Cat#SML1046 |
| Retinoic Acid | Sigma-Aldrich | Cat#R2625 |
| SAG | Cayman Chemicals | Cat#11914 |
| Compound E | Millipore | Cat#565790 |
| DAPT | Sigma-Aldrich | Cat#D5942 |
| db-cAMP | Millipore | Cat#28745 |
| Ascorbic Acid | Sigma-Aldrich | Cat#A4544 |
| BDNF | PeproTech | Cat#450-02 |
| GDNF | PeproTech | Cat#450-10 |
| L-glutamic acid | Sigma Aldrich | Cat#G1251 |
| Propidium Iodide | Thermo Fisher Scientific | Cat#P3566 |
| Dextran, Texas Red, 70,000 MW | Thermo Fisher Scientific | Cat#D1864 |
| Fluorescein isothiocyanate dextran, 500,000 MW | Sigma-Aldrich | Cat#FD500S |
| DTT | Sigma-Aldrich | Cat#D0632 |
| Actinomycin D | Sigma-Aldrich | Cat#A9415 |
| Cycloheximide | Sigma-Aldrich | Cat#C7698 |
| Protease Inhibitor Cocktail Set III, EDTA-free | Millipore | Cat#539134 |
| Complete Mini EDTA-free Protease Inhibitor Cocktail | Roche | Cat#11836170001 |
| TurboDNase | Thermo Fisher Scientific | Cat#AM2238 |
| RNaseOUT | Thermo Fisher Scientific | Cat#10777019 |
| RNase A | Thermo Fisher Scientific | Cat#EN0531 |
| Bovine Serum Albumin Fraction V | Sigma Aldrich | Cat#3117057001 |
| Ribonucleoside-Vanadyl Complex | New England BioLabs | Cat#S1402S |
| Salmon Sperm DNA | Thermo Fisher Scientific | Cat#15-632-011 |
| E.coli tRNA | Millipore | Cat#10109541001 |
| Critical Commercial Assays | ||
| Autofluorescence Eliminator Reagent | Millipore | Cat#2160 |
| P3 Primary Cell 4D Nucleofector Kit | Lonza | Cat#V4XP-3024 |
| Nuclei PURE Prep Nuclei Isolation Kit | Sigma-Aldrich | Cat#NUC201 |
| Streptavidin Coated Plates | Meso Scale Discovery | Cat#L45SA-2 |
| SuperSignal West Pico PLUS ECL Kit | Thermo Fisher Scientific | Cat#34580 |
| Immonilon ECL Ultra Western HRP Substrate | Millipore | Cat#WBULS0100 |
| BLOT-FASTSTAIN | G Biosciences | Cat#786-34 |
| RNeasy Mini Kit | Qiagen | Cat#74104 |
| Ambion TRIzol Reagent | Thermo Fisher Scientific | Cat#15-596-018 |
| SuperScript IV First-Strand Synthesis System | Thermo Fisher Scientific | Cat#18091050 |
| High-Capacity cDNA Reverse Transcription Kit | Thermo Fisher Scientific | Cat#4368814 |
| TaqMan Fast Advanced Master Mix | Thermo Fisher Scientific | Cat#44-449-64 |
| Experimental Models: Cell Lines | ||
| Human iPSC: EDi036-A | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs0594ictr-lbcnxx/ |
| Human iPSC: EDi037-A | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs0702ictr-lbcnxx/ |
| Human iPSC: EDi029-A | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs0188ictr-lbcnxx/ |
| Human iPSC: EDi034-A | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs0465ictr-lbcnxx/ |
| Human iPSC: EDi022-A | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs0617ictr-lbcnxx/ |
| Human iPSC: EDi044-A | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs1185ictr-lbcnxx/ |
| Human iPSC: CS1ATZ | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs1atzictr-nxx/ |
| Human iPSC: CS8PAA | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs8paaictr-nxx/ |
| Human iPSC: EDi043-A | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs1050ictr-lbcnxx/ |
| Human iPSC: CS0201 | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs0201ictr-nxx/ |
| Human iPSC: CS0002 | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs0002ictr-nxx/ |
| Human iPSC: CS9XH7 | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs9xh7ictr-nxx/ |
| Human iPSC: CS0BUU | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs0buuials-nxx/ |
| Human iPSC: CS7VCZ | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs7vczials-nxx/ |
| Human iPSC: CS0LPK | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs0lpkials-nxx/ |
| Human iPSC: CS6ZLD | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs6zldials-nxx/ |
| Human iPSC: CS8KT3 | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs8kt3ials-nxx/ |
| Human iPSC: CS2YNL | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs2ynlials-nxx/ |
| Human iPSC: CS0NKC | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs0nkcials-nxx/ |
| Human iPSC: CS6CLW | Cedars-Sinai Induced Pluripotent Stem Cell Core | https://biomanufacturing.cedars-sinai.org/product/cs6clwials-nxx/ |
| Human iPSC: 59-1 | Ababneh et al., 2019 | N/A |
| Human iPSC: OXC9-02-02 | Dafinca et al., 2016 | N/A |
| Human iPSC: 3231 | Justin Ichida | N/A |
| Human iPSC: 3-11 | Justin Ichida | N/A |
| Primary Human Astrocytes | ScienCell | Cat#1800-5 |
| HEK293T Cells | ATCC | Cat#CRL-11268; RRID: CVCL_1926 |
| Oligonucleotides | ||
| C9orf72 and Scrambled ASOs | Ionis Pharmaceutcials | N/A |
| C9orf72 Primers | Lagier-Tourenne et al., 2013; This Paper (Table S2) | N/A |
| DIG G4C2 FISH probe | Qiagen | N/A |
| DIG scrambled FISH probe | Qiagen | N/A |
| Nup50 TaqMan Gene Expression Assay | Thermo Fisher Scientific | Cat#Hs00855432_g1 |
| TPR TaqMan Gene Expression Assay | Thermo Fisher Scientific | Cat#Hs00162918_m1 |
| Nup98 TaqMan Gene Expression Assay | Thermo Fisher Scientific | Cat#Hs00180522_m1 |
| GP210 TaqMan Gene Expression Assay | Thermo Fisher Scientific | Cat#Hs00227779_m1 |
| NDC1 TaqMan Gene Expression Assay | Thermo Fisher Scientific | Cat#Hs00917927_m1 |
| POM121 TaqMan Gene Expression Assay | Thermo Fisher Scientific | Cat#Hs00208021_m1 |
| Nup107 TaqMan Gene Expression Assay | Thermo Fisher Scientific | Cat#Hs00220703_m1 |
| Nup133 TaqMan Gene Expression Assay | Thermo Fisher Scientific | Cat#Hs00217272_m1 |
| Nup62 TaqMan Gene Expression Assay | Thermo Fisher Scientific | Cat#Hs02621445_s1 |
| Nup205 TaqMan Gene Expression Assay | Thermo Fisher Scientific | Cat#Hs01046411_m1 |
| GAPDH TaqMan Gene Expression Assay | Thermo Fisher Scientific | Cat#Hs02786624_g1 |
| RPS18 TaqMan Gene Expression Assay | Thermo Fisher Scientific | Cat#Hs01375212_g1 |
| 18S rRNA TaqMan Gene Expression Assay | Thermo Fisher Scientific | Cat#Hs99999901_s1 |
| Recombinant DNA | ||
| Plasmid: pCMV6-AC-GFP-POM121 | Origene Technologies | Cat#RG235113 |
| Plasmid: pCMV6-AC-GFP-Nup133 | Origene Technologies | Cat#RG204410 |
| Plasmid: pCMV6-AC-GFP-Nup98 | Origene Technologies | Cat#RG213664 |
| Plasmid: pCMV6-AC-GFP-GP210 | Origene Technologies | Cat#RG213658 |
| Plasmid: pCMV6-AC-GFP-NDC1 | Origene Technologies | Cat#RG200141 |
| Plasmid: pEGFP-POM121 | Eilenberg Lab; Doucet et al., 2010; Talamas and Hetzer, 2011; Franks et al., 2016 | N/A |
| Plasmid: pQXCIB-sPOM121 | Franks et al., 2016 | N/A |
| Plasmid: pCMV6-AC-GFP-Trim21 | Origene Technologies | Cat#RG202088 |
| Plasmid: pLenti-NLS-tdTomato-NES | Zhang et al., 2015 | RRID: Addgene_112579 |
| Plasmid: pcDNA3.1-EGFP-(GA)50 | Wen et al., 2014 | N/A |
| Plasmid: pcDNA3.1-EGFP-(GR)50 | Wen et al., 2014 | N/A |
| Plasmid: pcDNA3.1-EGFP-(PR)50 | Wen et al., 2014 | N/A |
| Plasmid: pcDNA3.1+ 36RO | Mizielinska et al., 2014 | N/A |
| Plasmid: pcDNA3.1+ 106RO | Mizielinska et al., 2014 | N/A |
| Plasmid: pcDNA3.1+ 288 RO | Mizielinska et al., 2014 | N/A |
| Plasmid: 5’ UTR CGG 99x FMR1-EGFP | Addgene | Cat#63091; RRID: Addgene_63091 |
| Plasmid: pCTG202 | Nutter et al., 2019; Osborne and Thornton, 2008 | N/A |
| Plasmid: pCMV6-AC-GFP | Origene Technologies | Cat#PS100010 |
| Plasmid: mEGFP-N1 | Addgene | Cat#54767; RRID: Addgene_54767 |
| Plasmid: pmaxGFP | Lonza | Cat#V4XP-3024 |
| Software and Algorithms | ||
| FIJI | NIH | https://fiji.sc; RRID: SCR_002285 |
| Imaris | Bitplane | http://www.bitplane.com/; RRID: SCR_007370 |
| GraphPad Prism 7 | GraphPad Software | https://www.graphpad.com/; RRID: SCR_002798 |
| GraphPad Prism 8 | GraphPad Software | https://www.graphpad.com/; RRID: SCR_002798 |
| Zen 2 Pro | Carl Zeiss | https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html; RRID: SCR_013672 |
| Zen 2.1 | Carl Zeiss | https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html; RRID: SCR_013672 |
| Zen 2.3 SP1 | Carl Zeiss | https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html; RRID: SCR_018163 |
| Other | ||
| MTeSR | STEMCELL Technologies | Cat#85850 |
| IMDM | Life Technologies | Cat#12440053 |
| F12 | Life Technologies | Cat#11765062 |
| DMEM | Life Technologies | Cat#11995073 |
| Penicillin Streptomycin | Gibco | Cat#15140122 |
| NEAA | Life Technologies | Cat#11140-050 |
| B27 | Gibco | Cat#17504044 |
| N2 | Life Technologies | Cat#17502048 |
| Versene | Thermo Fisher Scientific | Cat#15040066 |
| ReLeSR | STEMCELL Technologies | Cat#05872 |
| EZ Pass Tool | Life Technologies | Cat#23181-010 |
| StemPro Accutase | Gibco | Cat#A11105-01 |
| Trypsin-EDTA | Life Technologies | Cat#25300054 |
| Matrigel | Corning | Cat#354230 |
| PureCol Type I Collagen Solution | Advanced BioMatrix | Cat#5005 |
| ACSF | Tocris | Cat#3525 |
| Normal Goat Serum | Vector Labs | Cat#S-1000; RRID: AB_2336615 |
| Donkey Serum | Sigma-Aldrich | Cat#D9663; RRID: AB_2810235 |
| ProLong Gold Antifade Reagent | Invitrogen | Cat#P36930 |
| ProLong Gold Antifade Reagent with DAPI | Life Technologies | Cat#P36931 |
| Hoescht | Thermo Fisher Scientific | Cat#H3570 |
| DAKO Protein Block Serum-Free | Dako | Cat#X0909 |
| Antibody Diluent with Background-Reducing Components | Dako | Cat#S302283-2 |
| OptiPrep Density Gradient Medium | Sigma-Aldrich | Cat#D1556 |
| RIPA | Sigma Aldrich | Cat#R0278 |
| NucBlue Live ReadyProbes | Thermo Fisher Scientific | Cat#R37605 |
| Slide-A-Lyzer MINI Dialysis Device, 20K MWCO | Thermo Fisher Scientific | Cat#88402 |
| Amicon Ultra-0.5 Centrifugal Filter Unit | Millipore | Cat#UFC510024 |
| NanoDrop 1000 Spectrophotometer | Thermo Fisher Scientific | N/A |
| Applied Biosystems Step One Plus Real Time PCR Machine | Thermo Fisher Scientific | Cat#4376600 |
| ImageQuant LAS 4000 | GE Healthcare | N/A |
| MESO QuickPlex SQ 120 | Meso Scale Discovery | N/A |
| CytoSpin 4 | Thermo Fisher Scientific | Cat#A78300003 |
| High Tolerance Coverslips | MatTek | Cat#PCS-170-1818 |
| Zeiss ELYRA S1 | Carl Zeiss | N/A |
| Zeiss LSM 800 with Airyscan | Carl Zeiss | RRID: SCR_015963 |
| Zeiss Apotome | Carl Zeiss | N/A |