KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-TDP43 | Proteintech | Cat# 10782-2-AP; RRID: AB_2892214 |
| Rabbit monoclonal anti-NeuN | Cell Signaling Technologies | Cat# 24307T RRID: AB_2651140 |
| Rabbit polyclonal anti-YTHDF2 | Proteintech | Cat# 24744-1-AP; RRID: AB_2687435 |
| Rabbit polyclonal anti-m6A | Millipore Sigma | Cat# ABE572; RRID: AB_2892213 |
| Rabbit monoclonal anti-m6A | Cell Signaling Technologies | Cat# 56593S; RRID: AB_2799515 |
| Rabbit polyclonal anti-m6A | Millipore Sigma | Cat# ABE572-I-100UG; RRID: AB_2892214 |
| Goat polyclonal anti-rabbit Alexa Fluor 488 | ThermoFisher | Cat# A-11034; RRID: AB_2576217 |
| Goat polyclonal anti-rabbit HRP | Jackson ImmunoResearch Labs Inc. | Cat# 111-035-003; RRID: AB_2313567 |
| Bacterial and virus strains | ||
| GIPZ Non-silencing Lentiviral shRNA Control | Horizon Discovery | #RHS4346 |
| GIPZ Lentiviral Human YTHDF2 shRNA | Horizon Discovery | #RHS4430-200182983 |
| Biological samples | ||
| Human post-mortem sample; Control 1 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 66 Sex: M |
| Human post-mortem sample; Control 2 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 85 Sex: M |
| Human post-mortem sample; Control 3 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 68 Sex: M |
| Human post-mortem sample; sALS 1 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 65 Sex: M |
| Human post-mortem sample; sALS 2 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 64 Sex: M |
| Human post-mortem sample; sALS 3 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 65 Sex: M |
| Human post-mortem sample; sALS 4 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 81 Sex: M |
| Human post-mortem sample; Control 4 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 76 Sex: F |
| Human post-mortem sample; Control 5 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 88 Sex: M |
| Human post-mortem sample; Control 6 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 56 Sex: M |
| Human post-mortem sample; ALS 1 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 66 Sex: F |
| Human post-mortem sample; ALS 2 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 64 Sex: M |
| Human post-mortem sample; ALS 3 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 68 Sex: M |
| Human post-mortem sample; Control 7 | University of Maryland Brain and Tissue Bank https://www.medschool.umaryland.edu/btbank/ | Experiment: m6A array Age: 48 Sex: M |
| Human post-mortem sample; ALS 4 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 76 Sex: M |
| Human post-mortem sample; ALS 5 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 60 Sex: F |
| Human post-mortem sample; ALS 6 | University of Michigan Brain Bank https://www.brainbank.umich.edu/ | Experiment: m6A array Age: 99 Sex: M |
| Chemicals, peptides, and recombinant proteins | ||
| Recombinant TDP43(WT) | Flores et al., 20197 | N/A |
| Deposited data | ||
| DART-seq data from HEK293T cells | This manuscript | https://www.ncbi.nlm.nih.gov/geo/ (SUB12370770) |
| Experimental models: Cell lines | ||
| HEK293T | ATCC | CRL-3216 |
| Primary rat neurons | Charles River Laboratories | Long-Evans rat (Crl:LE) |
| Human iPSCs | University of Michigan ALS Repository | 1021, 0883, 0312 |
| Human iPSCs | Cedars Sinai iPSC Repository | Cs29i, Cs29 |
| Human iPSCs (CLYBL:TO-hNgn1/2); Gene TARDBP WT; Tag TDP43-Dendra2-Carboxyl term | Weskamp et al., 202041 | Line 1021 Identifier: WT |
| Human iPSCs (CLYBL:TO-hNgn1/2); Gene TARDBP Mutation Isogenic M337V; Tag TDP43-Dendra2 Carboxyl term | Weskamp et al., 202041 Sidibé et al., 202157 |
Line 1021 Identifier: M337V |
| Human iPSCs (CLYBL:TO-hNgn1/2); Gene C9ORF72 Mutation | Weskamp et al., 202041 | Line 312 Identifier: C9ORF72 (#1) |
| Human iPSCs (CLYBL:TO-hNgn1/2); Gene C9ORF72 Mutation | Weskamp et al., 202041 | Line 883 Identifier: C9ORF72 (#2) |
| Human iPSCs (CLYBL:TO-hNgn1/2); Gene C9ORF72 Mutation | Weskamp et al., 202041 | Line Cs29i Identifier: C9ORF72 (#3) |
| Human iPSCs (CLYBL:TO-hNgn1/21); Gene C9ORF72 Mutation Isogenic corrected | Weskamp et al., 202041 Ho et al., 2021104 |
Line Cs29i Identifier: C9ORF72 ISO (#3) |
| Oligonucleotides | ||
| See Table S4 for complete list | ||
| Recombinant DNA | ||
| See Table S2 for complete list | ||
| Software and algorithms | ||
| RNAstructure software | Kierzek et al., 202243 | https://rna.urmc.rochester.edu/RNAstructure.html |
| Automated imaging and survival analysis | Malik et al., 2018101 | DOI: 10.5281/zenodo.7438867 DOI: 10.5281/zenodo.7438874 |
| Biorender | N/A | https://Biorender.com |
| Other | ||
| HaloTag ligand (JF646 dye) | Janelia Farms | https://www.janelia.org |