REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
GAPDH Monoclonal Anti GAPDH clone 71.1	Sigma Aldrich	Cat#G8795-200UL
TDP43 Polyclonal	Proteintech	Cat#10782-2-AP
BCAP31 (BAP31) Polyclonal	Proteintech	Cat#11200-1-AP
Chemicals, peptides, and recombinant proteins
Pladeinolide B	Biomol	Cat#Cay16538-100
4-Thiouridine	Chemgenes	Cat#N-RP-2304
Pierce High Sensitivity Strep-HRP	Thermo Fisher	Cat#21130
EZ-Link Biotin HPDP	Thermo Fisher	Cat#21341
Dynabeads MyOne Streptavidin C1	Thermo Fisher	Cat#65001
Critical commercial assays
Nuclei EZ Prep kit	Sigma Aldrich	Cat#NUC101-1KT
USB poly(A) length assay kit	Thermo Fisher	Cat#764551KT
TruSeq mRNA preparation kit	Illumina	Cat#RS-122-2102
SMARTScribe Reverse Transcriptase kit	Takara	Cat#639537
Advantage 2 DNA polymerase mix	Takara	Cat#639201
Deposited data
HeLa, iPSC, Organoid FLAM-seq data	Legnini et al.40	GEO: GSE126465
All FLAM-seq data generated in this work	This paper	GEO: GSE188539
Nascent Nanopore RNA data	Drexler et al.24	GEO: GSE123191
Experimental models: Cell lines
HEK Flp-In 293 T-Rex cells	Invitrogen	Cat#R78007
HeLa S3 cells	Rajewsky Lab	N/A
Experimental models: Organisms/strains
Mouse	MDC animal facility	C57BL/6N
Oligonucleotides
RT Primer 1: GGTAATACGACTCACTATAGCGA GANNNNNNNNNNCCCCCCCCCTTT	Legnini et al.40	N/A
RT primer 2: TGAGTCGGCAGAGAACTGGCGAA NNNNNNNNNNCCCCCCCCCTTT	Legnini et al.40	N/A
Template switching oligo (Iso-TSO): iCiGiCAAGCA GTGGTATCAACGCAGAGTACATrGrGrG	Legnini et al.40	N/A
PCR Primer 1 (RV, used in case RT Primer 1 was used): GGTAATACGACTCACTATAGCGAG	Legnini et al.40	N/A
PCR Primer 2 (RV, used in case RT Primer 2 was used): TGAGTCGGCAGAGAACTGGCGAA	Legnini et al.40	N/A
PCR Primer IIA (FW): AAGCAGTGGTATCAACGCAGAGT	Legnini et al.40	N/A
Software and algorithms
FLAMAnalysis	Rajewsky Lab Github	https://github.com/rajewsky-lab/FLAMAnalysis
Additional code used in this work	This paper	Mendeley data: https://doi.org/10.17632/drwmy4y8f5.1