KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-G3BP1	MBL International	Cat#RN048PW; RRID:AB_10794608
Mouse monoclonal anti-G3BP1	EMD Millipore	Cat#05–1938; RRID:AB_10561767
Rabbit polyclonal anti-TARDBP	Abnova	Cat#H00023435-A01; RRID:AB_461752
Rabbit polyclonal anti-Isl1/2	Santa Cruz Biotech	Cat#sc-30200; RRID:AB_2126589
Mouse monoclonal anti-SMI-31	EMD Millipore	Cat#NE1022; RRID:AB_2043448
Rabbit polyclonal anti-DAZAP1	Novus Biologicals	Cat#NBP1–82741; RRID:AB_11002177
Rabbit polyclonal anti-KAP1	Novus Biologicals	Cat# NBP2–39014
Mouse monoclonal anti-CUGBP1/CELF1	Novus Biologicals	Cat# NB200–316SS; RRID:AB_921076
Chemicals, peptides, and recombinant proteins
Dorsomorphin	Tocris	Cat#3093
SB431542	Tocris	Cat#1614
Retinoic Acid	Sigma	Cat#R2625
SAG	EMD Millipore	Cat#566660
DAPT	Tocris	Cat#2634
CHIR 99021	Tocris	Cat#4423
Purmorphamine	Tocris	Cat#4551
DMH-1	Tocris	Cat#4126
Valproic acid	Tocris	Cat#2815
Puromycin	Thermo Fisher	Cat#A1113803
Deposited data
CeFra-seq data	This paper	GEO: GSE157467
seCLIP data	This paper	GEO: GSE157467
Experimental models: cell lines
H9 ESCs (46, XX)	Yeo lab stocks	N/A
H1 ESCs (46, XY)	Yeo lab stocks	N/A
Kin2ALS6 iPSCs (46, XY)	Generated in-house, described in Fang et al., 2019	N/A
CV-B iPSCs (46, XY)	(Gore et al., 2011)	N/A
hnRNPA2/B1 D290V-1.1 hiPSC (46, XX) (also referred to as CR463.4)	Generated in-house, described in Martinez et al., 2016	N/A
hnRNPA2/B1 D290V-1.2 hiPSC (46, XX) (also referred to as CR464.2)	Generated in-house, described in Martinez et al., 2016	N/A
Software and algorithms
MaxQuant (version 1.6.0.16)	Cox and Mann, 2008	N/A
STAR (v2.4.0i)	Dobin et al., 2013	N/A
Cutadapt (v1.14)	(Martin, 2011)	N/A
CLIPper	Lovci et al., 2013	N/A
DeSeq2	Love et al., 2014	N/A
metaplotR	Olarerin-George and Jaffrey, 2017	N/A
featureCounts	Liao et al., 2014	N/A
Jellyfish (v2.0)	Marçais and Kingsford, 2011	N/A