KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-GFP	Immunology Consultants Laboratory	Cat#RGFP-45ALY
Mouse monoclonal anti-GAPDH	Millipore	Cat#MAB374; RRID: AB_2107445
Rabbit polyclonal anti-TDP43	Cell Signaling Technologies	Cat#3449; RRID: AB_2200511
Mouse monoclonal anti-puromycin	Sigma-Aldrich	Cat#MABE343; RRID: AB_2566826
Mouse monoclonal anti-GFP	Thermo Fisher	Cat#MA515256; RRID:AB_10979281
Rabbit monoclonal anti-mCherry	Abcam	Cat#ab213511
Chemicals, Peptides, and Recombinant Proteins
Recombinant TDP43(WT)	Dr. James Shorter	N/A
Recombinant TDP43(R151A) protein	This paper	N/A
Recombinant TDP43(D247A) protein	This paper	N/A
Critical Commercial Assays
Library generation for RNA-seq	Illumina TruSeq Stranded mRNA	RS-122-2101, RS-122-2102
Deposited Data
RNA-sequencing data	This paper	NCBI GEO (accession # GSE128647)
Experimental Models: Cell Lines
HEK293T	ATCC	CRL-3216
Long Evans rat embryonic day 19–20 mixed cortical primary neuron culture	Charles River Co.	Strain Code: 006
Experimental Models: Organisms/Strains
C. elegans: Bristol N2	CGC, University of Minnesota (https://cgc.umn.edu/strain/N2)	N2; RRID: WB-STRAIN:N2_(ancestral)
C. elegans: tdp-1 (R219A)	This paper	N/A
C. elegans: tdp-1 (ok803)	Vaccaro et al., 2012	RRID: WB-STRAIN:RB929
Oligonucleotides
Primers for cloning and site-directed mutagenesis, see Table S2	This paper	N/A
Labeled RNA/DNA sequences for EMSA	This paper	N/A
qPCR primers for RNA-IP	This paper	N/A
Recombinant DNA
Plasmid: pGW1-TDP43(WT)-EGFP	Barmada et al., 2010, 2014	N/A
Plasmid: pGW1-TDP43(WT)-Dendra2	Barmada et al., 2010, 2014	N/A
Plasmid: pGW1-TDP43(M337V)-EGFP	Barmada et al., 2010, 2014	N/A
Plasmid: pGW1-EGFP	Barmada et al., 2010, 2014	N/A
Plasmid: pGW1-mApple	Barmada et al., 2010, 2014	N/A
Plasmid: pFN21A-PUM2-R6SYE	Dr. Aaron Goldstrohm; Van Etten et al., 2012	N/A
Plasmid: pGW1-TDP43(PUM2)-EGFP	This paper	N/A
Plasmid: pGW1-TDP43(mPUM2)-EGFP	This paper	N/A
Plasmid: pHR-PP7-3xmCherry	Dr. Nils Walter; Yan et al., 2017	N/A
Plasmid: pGW1-TDP43(PP7)-EGFP	This paper	N/A
Plasmid: pGW1-TDP43(ΔRRM1-2)-EGFP	This paper	N/A
Plasmid: pGW1-TDP43(ΔRRM1)-EGFP	This paper	N/A
Plasmid: pGW1-TDP43(ΔRRM2)-EGFP	This paper	N/A
Plasmid: pGW1-TDP43(R151A)-EGFP	This paper	N/A
Plasmid: pGW1-TDP43(D247A)-EGFP	This paper	N/A
Plasmid: pGW1-TDP43(R151A, D247A)-EGFP	This paper	N/A
Plasmid: pGW1-TDP43(F147L, F149L)-EGFP	This paper	N/A
Plasmid: pGW1-TDP43(R151D)-EGFP	This paper	N/A
Plasmid: pGW1-TDP43(R151D, D247R)-EGFP	This paper	N/A
Plasmid: pGW1-TDP43(D247R)-EGFP	This paper	N/A
Plasmid: pGW1-TDP43(D247E)-EGFP	This paper	N/A
Plasmid: pGW1-TDP43(R151 A)-Dendra2	This paper	N/A
Plasmid: pGW1-TDP43(D247A)-Dendra2	This paper	N/A
Plasmid: pGW1-TDP43(F147L, F149L)-Dendra2	This paper	N/A
Plasmid: pGW1-TDP43(R151 D)-Dendra2	This paper	N/A
Plasmid: pGW1-TDP43(R151D, D247R)-Dendra2	This paper	N/A
Plasmid: pGW1-TDP43(D247R)-Dendra2	This paper	N/A
Plasmid: pGW1-TDP43(D247E)-Dendra2	This paper	N/A
Plasmid: pGW1-TDP43(WT)-Dendra2-CL1	This paper	N/A
Plasmid: pGW1-TDP43(PUM2)-Dendra2	This paper	N/A
Plasmid: pGW1-TDP43(PP7)-Dendra2	This paper	N/A
Plasmid: pGW1-TDP43(WT)-TEV-Halo	This paper	N/A
Plasmid: pE-6xHis-SUMO-TDP43(WT)	Dr. James Shorter	N/A
Plasmid: pE-6xHis-SUMO-TDP43(R151A)	This paper	N/A
Plasmid: pE-6xHis-SUMO-TDP43(D247A)	This paper	N/A
Software and Algorithms
FastQC v0.11.3	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/	RRID: SCR_015483
Tuxedo Suite	Langmead et al., 2009; Trapnell et al., 2009, 2013	RRID: SCR_013194
CummeRbund R package	http://compbio.mit.edu/cummeRbund/	RRID: SCR_014568
iPathwayGuide	http://advaitabio.com/ipathwayguide	N/A
HISAT2	Kim et al., 2015	RRID: SCR_015530
SGSeq	Goldstein et al., 2016	N/A
Limma	Ritchie et al., 2015	RRID: SCR_010943
Automated neuronal survival analysis	Malik et al., 2018	N/A
Automated neuronal measurements	Malik et al., 2018	N/A
Automated neuronal nuclear fractionation	Malik et al., 2018	N/A
WormLab	MBF Biosciences	N/A