REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-TDP-43 Antibody	Proteintech	Cat#10782-2-AP, RRID:AB_615042
Mouse anti-α-Tubulin Antibody	Sigma	Cat# T5168, RRID:AB_477579
Mouse anti-FLAG Antibody	Sigma	Cat#F1804, RRID:AB_262044
Rabbit anti-GFP Antibody	Abcam	Cat# ab290, RRID:AB_303395
IRDye 800CW Donkey anti-Rabbit IgG (H + L)	Li-Cor	Cat#926-32213, RRID:AB_621848
IRDye 680RD Goat anti-Mouse IgG (H+L)	Li-Cor	Cat#926-68070, RRID:AB_10956588
Bacterial and virus strains
NEB 5-alpha Competent E. coli (High Efficiency)	New England Biolabs	Cat#C2987I
Chemicals, peptides, and recombinant proteins
GFP-TRAP_MA beads	Chromotek	Cat#gtma-10
Protein G Dynabeads	Dynal	Cat#10004D
Protein A Dynabeads	Dynal	Cat#10002D
BSA	NEB	Cat#B9000S
DC Protein Assay Kit	Biorad	Cat#5000111
Phusion High-Fidelity DNA Polymerase (2 U/μL)	Thermo Fisher Scientific	Cat#F530L
10 mM dNTP Mix	Thermo Fisher Scientific	Cat#18427088
UltraPure Agarose	Thermo Fisher Scientific	Cat#16500500
Kanamycin Sulfate	Thermo Fisher Scientific	Cat#BP906-5
Ampicillin Sodium Salt	Sigma-Aldrich	Cat#A0166-5G
2,5-HEXANEDIOL, 99%,	Sigma-Aldrich	Cat#H11904-50G
1,6-Hexanediol	Sigma-Aldrich	Cat#240117-50G
Fast SYBR Green Master Mix	Thermo Fisher Scientific	Cat#4385612
TRIzol reagent	Thermo Fisher Scientific	Cat#15596206
VECTASHIELD	Vector labs	Cat#H-1000
Lipofectamine 2000 Transfection Reagent	Thermo Fisher Scientific	Cat#11668019
Lipofectamine RNAiMAX Transfection Reagent-1.5 mL	Thermo Fisher Scientific	Cat#13778150
AMPure XP, 5 mL	Agencourt	Cat#A63880
RIPA Buffer	Sigma-Aldrich	Cat#R0278-50ML
cOmplete(TM) Protease Inhibitor Cocktail	Sigma-Aldrich	Cat#11697498001
NuPAGE Novex 4-12% Bis-Tris Protein Gels, 1.0 mm, 10 well	Thermo Fisher Scientific	Cat#NP0321BOX
Puromycin	Takara Clontech	Cat#631305
Blasticidin S HCl	ThermoFisher Scientific	Cat#R21001
Hygromycin B (50mg/ml)	ThermoFisher Scientific	Cat#10687010
Doxycycline hydrate	Sigma-Aldrich	Cat#D9891
Zeocin Selection Reagent	Thermo Fisher Scientific	Cat#R25001
Novex TBE Gels, 6%, 10 well-1 box	Thermo Fisher Scientific	Cat#EC6265BOX
Critical commercial assays
SuperScript II Reverse Transcriptase	Thermo Fisher Scientific	Cat#18064014
Zero Blunt TOPO PCR Cloning Kit for Sequencing, with One Shot TOP10 Chemically competent E.coli	Thermo Fisher Scientific	Cat#K2875J10
QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina	Lexogen	Cat#015.2x96
QuantSeq-Flex First Strand Synthesis Module	Lexogen	Cat#SKU: 026.96
Fast SYBR Green Master Mix	Thermo Fisher Scientific	Cat#4385612
Maxwell RSC simplyRNA Cells Kit	Promega	Cat#AS1390
Deposited data
TDP-43 variant iCLIP in Hek-293	This study	Sequencing data deposited at EBI ArrayExpress under accession number "ArrayExpress: E-MTAB-9436"; Raw data processed on the iMaps webserver: https://imaps.goodwright.org/collections/868/
pAseq data	This study	Sequencing data deposited at EBI ArrayExpress under accession number "ArrayExpress: E-MTAB-9410"
Experimental models: Cell lines
Human: HEK293T cells	European Collection of Authenticated Cell Cultures (ECACC)	12022001
Oligonucleotides
Stealth RNAi siRNA Negative Control, Med GC	Thermo Fisher Scientific	Cat#12935300
TARDBP Stealth siRNA	Thermo Fisher Scientific	Cat#HSS177422
TDP43delCRrev	This study	CGCACCAAAGTTCATCCCACCACCCATA
TDP43delCRfw	This study	TCAGGCCCATCGGGTAATAACCAAAACCAAG
TDP43del274_320fw	This study	GCCATGATGGCTGCCGCCCA
TDP43del274_320rev	This study	ACTTCTTTCTAACTGTCTATTGCTATTGTGCTTAG
TDP43del367_414fw	This study	TAAACCCGCTGATCAgccTCGAC
TDP43del367_414rev	This study	GGCCTGGTTTGGCTCCCTCTG
hnRNPA2truncRv	This study	ACAGCGCTCGAGACTCCTAGAACTCTGA ACTTCCTGCAT
NLS-hnRNPA2fw	This study	acagcgAGATCTGATCCAAAAAAGAAGAG AAAGGTAGAGAAAACTTTAGAAACTGTT CCTTTGGAGAGGA
hybrid linker-TDP43LC-fw Xba1	This study	acagcgTCTAGACAAGAAATGCAGGAAGTT CAGTTAGAAAGAAGTGGAAGATTTGGTGGT
TDP43LC-rv Xho1	This study	acagcgCTCGAGCGGCCGCCACTG
NLS-pGEX-3x-hnRNPA2-fw	This study	acagcgAGATCTGATCCAAAAAAGAAGAGA AAGGTAGAGAGAGAAAAGGAACAGTTCC GTAAGCTCTTTA
pGEX-3x-hnRNPA2 fw	This study	acagcgAGATCTGAGAGAGAAAAGGAACAG TTCCGTAAGCTCTTTA
A2cMycNLS_ BsrGI_ pCDNA3_mCHerry_fw	This study	GACGAGCTGTACAAGcctgctgctaagagagt gaaactggatGAGAGAGAAAAGGAACAGTT CCGTAAG
A2trunc_EcoRI_ pCDNA3_mCHerry_rev	This study	CTGCAGAATTCTCAACTCCTAGAACTCT GAACTTCCTGC
A2TDPCTD_EcoRI_ pCDNA3_mCHerry_rev	This study	CTGCAGAATTCCTACATTCCCCAGCCA GAAGACT
TDP43fl_fw	This study	aaaaggatccATGgagcaaaagctcatttc
TDP43fl_rev	This study	aaaactcgaGCTACATTCCCCAGCCAGAAGACT
MH239_mutA326P_fw	This study	GATGGCTGCCCCCCAGGCAGCACTACA
MH240_mutA326P_rev	This study	TGTAGTGCTGCCTGGGGGGCAGCCATC
MH241_mutQ331K_fw	This study	AGGCAGCACTAAAGAGCAGTTGGGGTATGATG
MH242_mutQ331K_rev	This study	CATCATACCCCAACTGCTCTTTAGTGCTGCCT
MH243_mutG294A_fw	This study	GTAATAGCAGAGCGGGTGGAGCTGGTTTGGGAA
MH244_mutG294A_rev	This study	TTCCCAAACCAGCTCCACCCGCTCTGCTATTAC
MH251_mutG335A_fw	This study	TACAGAGCAGTTGGGCTATGATGGGCATG
MH252_mutG335A_rev	This study	CATGCCCATCATAGCCCAACTGCTCTGTA
MH253_mutM337P_fw	This study	CAGTTGGGGTATGCCGGGCATGTTAGC
MH254_mutM337P_rev	This study	GCTAACATGCCCGGCATACCCCAACTG
pJ4M_TDP-43 del272_320fw	This study	GCAATGATGGCGGCTGCACAA
pJ4M_TDP-43 del272_320rev	This study	GGAACGTTCCAGTTGGCGGT
pJ4M_TDP-43 316delUCR346fw	This study	TCAGGCCCGAGCGGCAATAATCAG
pJ4M_TDP-43 316delUCR346rev	This study	GGCACCAAAGTTCATACCGCCACCCA
pJ4M_TDP-43 320delQN366fw	This study	TTTGGTAGCGGTAACAATAGCTACAGCG
pJ4M_TDP-43 320delQN366rev	This study	CGGATTGATGGAGAAGGCACCAAAG
pJ4M_TDP-43 320del414rev	This study	CGGATTGATGGAGAAGGCACCAAAGTTCA
pJ4M_TDP-43 367del414rev	This study	CGCTTGATTCGGTTCACGCTGCATGT
SMC1A PAS distal_fw	(Rot et al., 2017)	caaccaaagaagtcacgtacca
SMC1A PAS distal_rev	(Rot et al., 2017)	aattgtgctcgtccataaagg
SMC1A PAS prox_fw	(Rot et al., 2017)	GTTCTACACCAAGGCCGAGA
SMC1A PAS prox_rev	(Rot et al., 2017)	TCGAAGGTCAGGACTTTGCT
PPP2R2D GE fw	This study	TTGAGTGTTGCTGGAACGGT
PPP2R2D GE rev	This study	TACACACCTTCCGGGGTTTG
PPP2R2D APA fw	This study	TGATTGCCTGTGCCCCTG
PPP2R2D APA rev	This study	TAGACAGGGGGATGGGATGG
GPCPD1 GE fw	This study	AGCAGGAATTGCCAGAGCTT
GPCPD1 GE rev	This study	ACTGAGAAGCCCAAAAGGCA
GPCPD1 dist fw	This study	GGAAAGTGTTGTGGCGCTTC
GPCPD1 dist rev	This study	TGGATGGGAGACGACAGACA
GXYLT1 GE fw	This study	TGACGATAAGCAACCAGCAT
GXYLT1 GE rev	This study	TGGTGATCTGGCATAACGATCT
GXYLT1 APA fw	This study	AGGGTCCCTGGTCAGACATT
GXYLT1 APA rev	This study	ACAAGAGGTTGCTATAGTGTGCT
ATG4B fw	(Ling et al., 2015)	TGTGTCTGGATGTGAGCGTG
ATG4B rev	(Ling et al., 2015)	TCTAGGGACAGGTTCAGGACG
GAPDH qPCR fw	This study	AATCCCATCACCATCTTCCAG
GAPDH qPCR rev	This study	AAATGAGCCCCAGCCTTC
Recombinant DNA
pcDNA 3.1(+) Mammalian Expression Vector	Thermo Fisher Scientific	Cat#V79020
pOG44 Flp-Recombinase Expression Vector	Thermo Fisher Scientific	Cat#V600520
pcDNA5 FRT/TO Vector Kit	Thermo Fisher Scientific	Cat#V652020
Software and algorithms
Fiji/ImageJ	Rueden et al., 2017	https://imagej.nih.gov/ij/
GraphPad Prism 5	GraphPad Software	https://www.graphpad.com/scientific-software/prism/
R v 4.0.3	The R Project for Statistical Computing	https://www.r-project.org/
Python v 3.7	Python Software Foundation	https://www.python.org
Snakemake v 5.31.1	Mölder et al., 2021	https://snakemake.github.io/
iCount; iMaps	König et al., 2010	https://github.com/tomazc/iCount
iCLIP analysis code; pAseq analysis pipeline and code	This study	https://github.com/ulelab/tdp43-mutants