library_construction_protocol: eCLIP was performed as previously described (Blue SB, et al. Nature Protocols 2022). Briefly, 10 million HeLa cells were UV crosslinked (254 nM, 400 mJ/cm2), snap frozen, and lysed as previously described. RNA fragmentation was performed, 2% of the sample was removed for size-matched input, and the remainder was subjected to immunoprecipitation of TDP43-bound RNA with antibody against TDP43 (Proteintech 10782-2-AP). Dephosphorylation, RNA adapter ligation, SDS-PAGE electrophoresis and nitrocellulose membrane transfer, RNA isolation, reverse transcription, and PCR amplification were performed as previously described (Blue, SM. et al, Nat Protocols 2022). Libraries are as previously described for eCLIP (Blue, SM. et al, Nat Protocols 2022), based on the Illumina RNA TruSeq HT adapter strategy.