REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Sox2 monoclonal antibody (D6D9) Alexa 647-conjugated	Cell Signaling	Cat no. 5067; RRID: AB_10828229
Sox2 monoclonal Antibody	Cell Signaling	Cat no. 2748S; RRID: 823640
Nanog monoclonal Antibody	Cell Signaling	Cat no. 8822; RRID: AB_11217637
TDP-43 polyclonal Antibody	Sigma-Aldrich	Cat no. SAB4200006; RRID: AB_10610848
TDP-43 polyclonal Antibody	Proteintech Group	Cat no. 10782-2-AP; RRID: AB_615042
GFP polyclonal Antibody	Molecular Probes/Thermo Fisher	Cat no. A6455; RRID: AB_221570
SFPQ monoclonal Antibody	Thermo Fisher Scientific	Cat no. MA1-25325; RRID: AB_2186931
NONO polyclonal Antibody	Abcam	Cat no. ab70335; RRID: AB_1269576
CPEB1 polyclonal Antibody	Cell Signaling	Cat no. 13583
PSPC1 rabbit polyclonal antibody	Naganuma et al., 2012
SRSF3 polyclonal antibody	ProteinTech Group	Cat no. 10916-1-AP; RRID: AB_2185064
TNPO1 monoclonal antibody	Abcam	Cat no. ab10303; RRID: AB_2206878
U2AF2 monoclonal antibody	Sigma-Aldrich	Cat no. U4758; RRID: AB_262122
Brachyury N-19 goat polyclonal antibody	Santa Cruz Biotechnologies	Cat no. sc17743; RRID: AB_634980
Foxa2 (HNF-3β) M-20 goat polyclonal	Santa Cruz Biotechnologies	Cat no. sc-6554; RRID: AB_2262810
RFP rabbit polyclonal	Rockland	Cat no. 600-401-379S; RRID: AB_2209751
Donkey anti-rabbit IgG 555	Invitrogen	Cat no. A31572; RRID: AB_162543
Donkey anti-goat IgG 488	Invitrogen	Cat no. A11055; RRID: AB_2534102
Histone H3 polyclonal Antibody	Abcam	Cat no. ab1791; RRID: AB_302613
Beta Actin polyclonal Antibody	New England Biolabs/Cell Signaling antibody	Cat no. 8H10D10; RRID: AB_2242334
RNAPolII-S5,S2	Abcam	Cat no. ab103968; RRID: AB_2687918
DyLight 650-conjugated anti SSEA-1 (clone MC-480)	Thermo Fisher	Cat no. MA1-022-D650; RRID: AB_2536696
Alexa Fluor 647-conjugated anti TRA-1-60	BD Bioscience	Cat no. 560122; RRID: AB_1645448
Alexa Fluor 647 Dk anti-Gt IgG (H+L)	Thermo Fisher	Cat no. A11058; RRID: AB_2534105
Goat anti-rabbit IgM-HRP	Santa Cruz Biotechnology	Cat no. sc-2030; RRID: AB_631747
Goat anti-mouse IgG HRP-conjugated	Dianova	Cat no. 115-035-003; RRID: AB_10015289
Chemicals, Peptides, and Recombinant Proteins
(Z)-4-Hydroxytamoxifen	Sigma-Aldrich	H7904
Neurobasal Medium	Thermo Fisher	21103049
DMEM F12	Thermo Fisher	11320033
N2	Thermo Fisher	17502048
B27	Thermo Fisher	17504044
Glutamax	Thermo Fisher	35050
1% nonessential amino acids	Thermo Fisher	1140050
2-mercaptoethanol	Thermo Fisher	31350-010
MEK inhibitor PD0325901	Axon Medchem	1408
GSK3 inhibitor CHIR99021	Tocris	4953/50
LIF	produced in house	SV30160.03HI
Trypsin-EDTA	Thermo Fisher	25200056
HyClone Fetal Bovine Serum (FBS)	GE Healthcare	SV30160.03HI
mTeSR1 medium	Stem Cell Technologies	058-50
Matrigel	Cornig	356234
Gentle Cell Dissociation Reagent	StemCell Technologies	7174
KnockOut Serum Replacement	Thermo Fisher	10828028
DMEM high glucose	Thermo Fisher	11965092
Blue Sepharose 6 Fast Flow/ HisTrap HP columns	GE LifeSciences	17-0412-01
recombinant WNT3A	D. Ten Berge	N/A
Retinoic Acid	R2625-50MG	Sigma
recombinant BMP4	R&D systems	314-BP
Accutase	Sigma-Aldrich	A6964
Y-27632 ROCK inhibitor	R&D systems	1254/10
RPMI1640	Thermo Fisher	11875093
L-Glutamine	Thermo Fisher	25030081
B27 supplement without insulin	Thermo Fisher	A1895601
Lipofectamine 3000	Thermo Fisher	L3000008
Lipofectamine RNAiMAX	Thermo Fisher	13778150
Puromycin	Sigma-Aldrich	P8833-10MG,
blasticidine	Invivogen	ant-bl-05
G418	Invivogen	ant-gn-01
Trizol LS	Life Technologies	10296028
QIAzol	QIAGEN	79306
Zymo Direct-zol	Zymogen	R2052
RNeasy Mini Kit	QIAGEN	74104
SuperScript III Reverse Transcriptase	Thermo Fisher	18080085
RNase H, recombinant	New England Biolabs	M0297S
miRNeasy Micro Kit	QIAGEN	217084
KOD FX Neo enzyme	Toyobo	KFX-201
Taqman assay master mixl	Thermo Fisher	4369514
Q5® High-Fidelity 2X Master Mix	Thermo Fisher	M0492
miScript PCR Starter Kit	QIAGEN	218193
formamide	Calbiochem	4610-OP
Dextran Sulfate	VWR	9011-18-1
competitor tRNA from E.coli	Roche Diagnostics	10109541001
methanol-free formaldehyde	Thermo Fisher	28906
digoxigenin (DIG) RNA labeling kit	Roche	11175025910
2-well μ-Slides	Ibidi	80286
8-chambr Slides	Ibidi	80826
DAPI	New England Biolabs	9071S
SYTOX Blue Dead Cell Stain, for flow cytometry	Thermo Fisher	S34857
UltraPure BSA	Thermo Fisher	AM2616
vanadyl-ribonucleoside complex	New England Biolabs	S1402S
Insulin (human recombinant - yeast)	Life Tech	12585-014
Transferrin (human recombinant)	Sigma-Aldrich	T3705-1G
Sodium selenite	Sigma-Aldrich	S5261-10G
Ascorbic acid 2-phosphate	Sigma-Aldrich	A8960-5G
FGF2 (human recombinant - E. coli)	Peprotech	100-18B (1 mg)
TGFB (human recombinant - E. coli)	Peprotech	100-21 (100 ug)
TURBO Dnase	Thermo Fisher	am2238
RNeasy MinElute RNA cleanup	QIAGEN	74204
protease inhibitors	Merck Millipore	539134
phosphatase inhibitors	Sigma-Aldrich	4906837001
proteasome inhibitor	Sigma -Aldrich	MG132
Mini-PROTEAN TGX Stain Free Gels, 4-15%	Bio-Rad Laboratories	456-8086
Clarity Western ECL Substrate	Bio-Rad Laboratories	170-5060
5% milk powder	Carl Roth	T145.1
RNasin Plus RNase inhibitor	Promega	PRN2615
Lys-C	Wako Chemicals	125-02543
Trypsin	Promega	V5111
Igepal CA-630	Sigma-Aldrich	I8896
Triton X-100	Sigma-Aldrich	9002-93-1
Protein A Dynabeads	Thermo Fisher	10002D
RNase I	Ambion	AM2295
RNase A	Nacalai Tesque	9001-99-4
Proteus Clarification Mini Spin Column	Generon	GEN-MSF500
ssRNA ligase	New England Biolabs	M0204S
PEG400	Sigma-Aldrich	202398
sodium butyrate	Sigma-Aldrich	B5887-250MG
ascorbic acid	Sigma-Aldrich	A8960
Hydrocortisone	Sigma-Aldrich	H0396
Insulin	Thermo Fisher	12585014
Protan BA85 Nitrocellulose Membrane	Thermo Fisher	LC2009
proteinase K	Roche	3115828001
Phase Lock Gel Heavy tube	713-2536	VWR
Glycoblue coprecipitant	Ambion	9516
Costar SpinX column	Corning Incorporated	8161
CircLigase ssDNA	Epicenter	CL4111K
Accuprime Supermix 1	Thermo Fisher	Accuprime Supermix 1
Agencourt AMPure XP beads	Beckman-Coulter	Agencourt AMPure XP beads
Critical Commercial Assays
P3 Primary Cell 4D-Nucleofector Kit	Lonza	V4XP-3012
Nucleofector Kit V	Lonza	VCA-1003
RiboZero	Epicenter	Cat# MRZG12324
TruSeq stranded total RNA Sample Prep Kit	Illumina	Cat# 20020599
QuantSeq mRNA 3′ end sequencing kit	Lexogen	Cat# SKU 015.96 and SKU 016.96
alkaline phosphatase staining	Sigma-Aldrich	AB0300-1KT
Agilent 2100 Bioanalyzer with RNA Pico 6000 kit	Agilent	5067-1513
Qubit dsDNA HS Assay Kit	Thermo Fisher	Q32854
Inside Stain kit	Miltenyi Biotech	130-090-477
Nucleofector MEF 1 Kit	Lonza	VPD-1004
Nascent RNA Capture Kit	Thermo Fisher	C10365
Deposited Data
QuantSeq and RNaseq libraries to study developmental alternative polyadenylation in hESC, its progeny and upon TDP-43 KD	This paper	E-MTAB-5090. Accessible via https://www.ebi.ac.uk/arrayexpress/
RNaseq libraries to study developmental alternative polyadenylation in human primitive streak progenitors derived from hESCs.	This paper	E-MTAB-5099. Accessible via https://www.ebi.ac.uk/arrayexpress/
QuantSeq libraries to study TDP-43 dependent alternative polyadenylation in mESCs and upon paraspeckles/TDP43 perturbations	This paper	E-MTAB-5091. Accessible via https://www.ebi.ac.uk/arrayexpress/
RNaseq libraries to study TDP-43 dependent alternative polyadenylation in mESCa and cTdp43KO	This paper	E-MTAB-5097. Accessible via https://www.ebi.ac.uk/arrayexpress/
iCLIP datasets for TDP-43	This paper	E-MTAB-5100. Accessible via https://www.ebi.ac.uk/arrayexpress/
Nascent RNaseq in conjunction with Illumina TRUseq method to sequence total RNAs including short lived RNAs using highly strand-specific next-generation sequencing (NGS) libraries	This paper	E-MTAB-5115
QuantSeq libraries to study gene expression changes in Neat1ΔpA compared to parental undifferentiated hESCs	This paper	Accessible via https://expressrna.org/
Fractionation RNaseq in conjunction with Illumina TRUseq method	This paper	E-MTAB-5116
RNaseq differentiation of hESCs to endoderm, mesoderm, ectoderm, and hepatoblasts	Gifford et al., 2013	GSM1112847, GSM1112845, GSM1112846, GSM1112844, GSM1112835, GSM1112833, GSM1112834, GSM1112837, GSM1124072, GSM1124072
iCLIP datasets for TDP-43 in SH-SY5Y cells	Tollervey et al., 2011	E-MTAB-527 Accessible via https://www.ebi.ac.uk/arrayexpress/
Analysis of Pro-Inflammatory Gene Activation and RNA Processing by RNaseq of Nascent Transcripts I		GSE32916 and GSE38892, accessible via GEO accession viewer
Mendeley dataset; Additional data composed of Sanger sequencing and confirmatory gel electrophoresis confirming the CRISPR-Cas9 edited human and mouse embryonic stem cells.	This paper and Mendeley data	https://data.mendeley.com/datasets/hbr8p7n526/2
Experimental Models: Cell Lines
HEK293 Flag-WT TDP-43 tetracycline inducible	Budini et al., 2015
HeLa	ATCC: CCL-2	RRID: CVCL_0045
primary neonatal human dermal fibroblast (NHDF)	ATCC	CRL-2522
secondary human fiboblasts (HiF-Ts)	Cacchiarelli et al., 2015
HAP1	ATCC	204508
hESCs H9	Wicell	WB66593
V6.5 mESCs	ATCC	SCRC-2011
e14tg2a ICE	ATCC	SCRC-1029
cTdp-43 KO	Ling et al., 2015
IDG3.2	Hitz et al., 2007 (C57BL/6J x 129S6/SvEvTac)F1 mESC line
Experimental Models: Organisms/Strains
Mouse: CD-1	Charles River	Mouse: CD-1
Mouse: mT/mG	Muzumdar et al., 2007	Mouse: mT/mG
Oligonucleotides
Stellaris smFISH Probe: Human NEAT1 Middle Segment with Quasar 570	Stellaris	SMF-2037-1-BS
Stellaris smFISH Probe: Human NEAT1 5` segment conjugated to Quasar®670 or Quasar®570	Stellaris	SMF-2036-1
Stellaris smFISH Probe: Mouse Neat1 middle segment conjugated to Quasar®670	Stellaris	Customized product
Stellaris smFISH Probe: Mouse Neat1 5` segment conjugated to Quasar®570	Stellaris	Customized product
Stealth RNAi siRNA	Thermo Fisher Scientific	12935-200
TDP-43 siRNA, 5′-GGCUCAAGCAUGGAUUCUA-	Dharmacon	Customized product
GAPDH_F		GCTCATTTCCTGGTATGACAACG
GAPDH_R		GAGATTCAGTGTGGTGGGGG
OCT4_F		CAATTTGCCAAGCTCCTGAAG
OCT4_R		AAAGCGGCAGATGGTCGTT
MESP_F		CTGCCTGAGGAGCCCAAGT
MESP_R		GCAGTCTGCCAAGGAACCA
T_F		CAACCTCACTGACGGTGAAAAA
T_R		ACAAATTCTGGTGTGCCAAAGTT
MIXL_F		CCGAGTCCAGGATCCAGGTA
MIXL_R		CTCTGACGCCGAGACTTGG
SOX17_F		GGCGCAGCAGAATCCAGA
SOX17_R		CCACGACTTGCCCAGCAT
Lefty1_F		TGTACATTGACCTGCAGGG
Lefty1_R		ACTCATAAGCCAGGAAGCC
EOMES_F		ACAGGAGATTTCATTCGGG
EOMES_R		TTGTAAGACTATCATCTGGGTG
GDF3_F		GAGACTTATGCTACGTAAAGGA
GDF3_R		GGTAAAGAAAGAAACCTTGGTC
FOXD3_F		CTACTACAGGGAGAAGTTCCC
FOXD3_R		GTTGAGTGAGAGGTTGTGG
Neat1.screen_F		GTTTGGCTTGAATGGTGCTT
Neat1.screen_R		CTTCCCTCCCAGAGAGTTGA
NEAT1pA.screen_F		TGAGCCAAGACTAGAGGGGA
NEAT1pA.screen_R		CCTTGCTGCTCCCTTTGAAA
Neat1.screen_F		GTTTGGCTTGAATGGTGCTT
Neat1.screen_R		CTTCCCTCCCAGAGAGTTGA
Sox2Δmir21.screen_F		TTAACGCAAAAACCGTGATG
Sox2Δmir21.screen_R		GGCAGCCTGATTCCAATAAC
Neat1ΔTH.screen_F		TTACTGCACCAGACCCTGTC
Neat1ΔTH.screen_R		TCCTTTGGGGAACAGGAAAGAG
Gapdh_F		TTCACCACCATGGAGAAGGC
Gapdh_R		CCCTTTTGGCTCCACCCT
Neat1_1_F		TTGGGACAGTGGACGTGTGG
Neat1_1_R		TCAAGTGCCAGCAGACAGCA
Neat1_2_F		GATCGGGACCCCAGTGACCT
Neat1_2_R		AGCTTTCCCCAACACCCACA
mmu-mir-21	QIAGEN	MIMAT0000076: 5′UAG CUU AUC AGA CUG AUG UUG A, MIMAT0004494: 5′CAA CAC CAG UCG AUG GGC UGU
TaqMan Gene Expression Assay NEAT1, isoform v2	Thermo Fisher	Hs03924655_s1
TaqMan Gene Expression Assay, Gene Symbol: SOX2	Thermo Fisher	Hs01053049_s1
TaqMan Gene Expression Assay, Gene Symbol: GAPDH	Thermo Fisher	Hs02758991_g1
TaqMan Gene Expression Assay, Neat1, Gene Symbol NEAT1 isoform v1	Thermo Fisher	Hs01008264_s1
TaqMan Gene Expression Assay, Gene Symbol POU5F1	Thermo Fisher	Hs00999632_g1
TaqMan® Gene Expression Assay, Gene Symbol SCARNA10	Thermo Fisher	Hs03309805_s1
TaqMan® Gene Expression Assays, gene symbol Neat1v1	Thermo Fisher	Mm03455878_s1
Recombinant DNA
pmaxGFP plasmid with insertions of modified SOX2-UTR	Addgene	16007
PMIRH21PA-1-GVO-SBI	System Biosciences	PMIRH21PA-1-GVO-SBI
PX330-B/B	Addgene	42230
pcDNA6/TR	Addgene	5676
pCXLE-hMLN	Addgene	27079
MIP 247 CoMiP 4in1 with shRNA p53.	Addgene	63726
Software and Algorithms
Bowtie2		http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
TopHat2		RRID: SCR_013035; http://tophat.cbcb.umd.edu/
STAR	Dobin et al., 2013	RRID: SCR_015899; https://github.com/alexdobin/STAR
Cufflinks		RRID: SCR_014597; http://cole-trapnell-lab.github.io/cufflinks
expressRNA	Rot et al., 2017	http://www.expressrna.org/
BLAST+/2.3.0		RRID: SCR_001598; https://blast.ncbi.nlm.nih.gov/Blast.cgi
R	R Project for Statistical Computing	RRID: SCR_001905; http://www.r-project.org/
DEXseq		https://github.com/roryk/DEXSeq/
Progenesis QI software	version 2.0, Nonlinear Dynamics
Mascot (version 2.5.1)	Matrix Science	http://www.matrixscience.com/whats_new/mascot-2-5-1-patch-release.html
EdgeR	Robinson et al., 2010	https://bioconductor.org/packages/release/bioc/html/edgeR.html
iCount		http://icount.fri.uni-lj.si/
HTSeq		https://htseq.readthedocs.io/en/release_0.11.1/
Other
NEATΔpA.gRNA.up.fwd		CACCGATGCAAACAATTACTGTCGT
NEATΔpA.gRNA.up.rev		AAACACGACAGTAATTGTTTGCATC
NEATΔpA.gRNA.down.fwd		CACCGTGTTGAGAGTTGGTAATCAT
NEATΔpA.gRNA.down.rev		AAACATGATTACCAACTCTCAACAC
Neat1ΔpA.gRNA.up.fwd		caccGAAGCTTCTTAGAATTGTCA
Neat1ΔpA.gRNA.up.rev		aaacTGACAATTCTAAGAAGCTTC
Neat1ΔpA.gRNA.down.fwd		caccGAGGGGAGGAAAATGGTTAGT
Neat1ΔpA.gRNA.down.rev		aaacACTAACCATTTTCCTCCCCTC
Neat1ΔTDP43.gRNA.up.fwd		caccgTTGTGAAAACCCTGTATATG
Neat1ΔTDP43.gRNA.up.rev		aaacCATATACAGGGTTTTCACAAc
Neat1ΔTDP43.gRNA.down.fwd		caccGTGAAGAAAGCTGTAACTGC
Neat1ΔTDP43.gRNA.down.rev		aaacGCAGTTACAGCTTTCTTCAC
Sox2Δmir21_gRNA1_up		caccgAGTATTTATCGAGATAAACA
Sox2Δmir21_gRNA1_down		aaacTGTTTATCTCGATAAATACTc
Sox2Δmir21_gRNA2_up		caccgATTTAGGACCGTTACAAACA
Sox2Δmir21_gRNA2_down		aaacTGTTTGTAACGGTCCTAAATc
Neat1ΔTH_gRNA1_fwd		caccgaaggaagcacggtactgca
Neat1ΔTH_gRNA1_rev		AAACtgcagtaccgtgcttccttc
Neat1ΔTH_gRNA2_fwd		caccgAGGAAAAGAAACACCTGCGG
Neat1ΔTH_gRNA2_rev		aaacCCGCAGGTGTTTCTTTTCCTc