REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-MAP2	Sigma Aldrich	Catalog number M4403; RRID: AB_477193
Rabbit polyclonal anti-TAU	Synaptic System	Catalog number 314 002; RRID: AB_993042
Mouse monoclonal anti-SMI32	Abcam	Catalog number ab7795; RRID: AB_306084
Rabbit polyclonal anti-MNX1 (HB9)	Merck Millipore	Catalog number ABN174; RRID: AB_2732012
Mouse monoclonal anti-HUD (E-1)	Santa Cruz Biotechnology	Catalog number sc-28299; RRID: AB_627765
Mouse monoclonal Anti-β-Tubulin III	Sigma Aldrich	Catalog number T8578; RRID: AB_1841228
Mouse monoclonal anti-eEF1A1, clone CBP-KK1	Merck Millipore	Catalog number 05-235; RRID: AB_309663
Rabbit polyclonal anti eIF4A2	Abcam	Catalog number ab31218; RRID: AB_732123
Rabbit polyclonal anti-PABP	Abcam	Catalog number ab21060; RRID: AB_777008
Mouse monoclonal anti-DCP1A	Abcam	Catalog number ab57654; RRID: AB_942144
Mouse monoclonal Anti-TIA-1	Santa Cruz Biotechnology	Catalog number sc-166247; RRID: AB_2201545
Mouse monoclonal anti-Oct4 (C-10)	Santa Cruz Biotechnology	Catalog number sc-5279; RRID: AB_628051
Mouse monoclonal anti-Nestin, (clone rat-401)	Merck Millipore	Catalog number MAB353; RRID: AB_94911
Mouse monoclonal anti-β-Tubulin III	Promega	Catalog number G712A
Goat anti-Rabbit IgG (H+L) polyclonal, Cross-Adsorbed Secondary Antibody, Alexa Fluor 488	Thermo Fisher Scientific	Catalog number A-11008; RRID: AB_143165
Goat anti-Rabbit IgG (H+L) polyclonal, Cross-Adsorbed Secondary Antibody, Alexa Fluor 594	Thermo Fisher Scientific	Catalog number A-11012; RRID: AB_2534079
F(ab)2-Goat anti-Mouse IgG (H+L) polyclonal, Cross-Adsorbed Secondary Antibody, Alexa Fluor 488	Thermo Fisher Scientific	Catalog number A-11017; RRID: AB_2534084
F(ab)2-Goat anti-Mouse IgG (H+L) polyclonal, Cross-Adsorbed Secondary Antibody, Alexa Fluor 594	Thermo Fisher Scientific	Catalog number A-11020; RRID: AB_2534087
Donkey anti-Rabbit IgG (H+L) polyclonal, Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488	Thermo Fisher Scientific	Catalog number A-21206; RRID: AB_2535792
Donkey anti-Goat IgG (H+L) polyclonal, preadsorbed Secondary Antibody, Alexa Fluor 594	Abcam	Catalog number ab150136
mouse monoclonal anti-β-tubulin (3F3-G2)	Santa Cruz Biotechnology	Catalog number sc-53140; RRID: AB_793543
Rabbit polyclonal anti-HA	Bethyl laboratories	Catalog number A190-108A; RRID: AB_67465
Rabbit polyclonal anti-eIF4A1	Abcam	Catalog number ab31217; RRID: AB_732122
Rabbit anti-eIF4A3	Home made by Prof. Macchi’s Lab
Rabbit polyclonal anti-eEF1A1	Sigma Aldrich	Catalog number SAB2108050
Rabbit polyclonal anti-PABPC1	Sigma Aldrich	Catalog number SAB2101708; RRID: AB_10604467
Rabbit polyclonal anti-Rpl26	Abcam	Catalog number ab59567; RRID: AB_945306
Rabbit monoclonal anti-S6	Cell Signaling Technology	Catalog number 2217; RRID: AB_331355
Bacterial and Virus Strains
XL1 Blue	Stratagene	Catalog number 200249
DH5alpha	This study	N/A
Chemicals, Peptides, and Recombinant Proteins
Doxycycline	Sigma-Aldrich	Catalog number A3656
Torin1	EMD MILLIPORE	Catalog number 475991
Sodium arsenite solution	EMD MILLIPORE	Catalog number 1.06277
Cycloheximide (CHX)	Sigma-Aldrich	Catalog number C7698
Phorbol 12-myristate 13-acetate (PMA)	Sigma-Aldrich	Catalog number P8139
Dimethyl Sulfoxide (DMSO)	Fisher Scientific	Catalog number BP2311
NGF	Sigma-Aldrich	Catalog number N6009
GDNF	Peprotec	Catalog number 450-44-10
CNTF	Peprotec	Catalog number 450-13-10
BDNF	Peprotec	Catalog number 450-02-10
Collagen type IV	Sigma-Aldrich	Catalog number C5533
Laminin Mouse Protein, Natural	Thermo Fisher Scientific	Catalog number 23017015
Lectin Sigma L9640	Sigma-Aldrich	Catalog number L9640
Poly-DL-ornithine hydrobromide	Sigma-Aldrich	Catalog number P8638
Recombinant His-HuD protein	This study	N/A
Critical Commercial Assays
Pierce Anti-HA Magnetic Beads	Thermo Fisher Scientific	Catalog number 88836
IBA Lifesciences Ni-NTA Superflow	Fisher Scientific	Catalog number 2-3206-025
Pierce Anti-HA Agarose Beads	Thermo Fisher Scientific	Catalog number 26181
Streptavidin MyOne T1 beads	Thermo Fisher Scientific	Catalog number 65601
ECL Prime Western Blotting System GE Healthcare	Sigma-Aldrich	Catalog number GERPN2232
Bradford Reagent	Sigma-Aldrich	Catalog number B6916
Lipofectamine RNAiMAX Reagent	Thermo Fisher Scientific	Catalog number 13778030
Lipofectamine 2000	Thermo Fisher Scientific	Catalog number 11668027
Dual-Glo Luciferase Assay System	Promega	Catalog number E2920
Retinoic acid	Sigma-Aldrich	Catalog number R2625
Click-iT AHA Alexa Fluor Protein Synthesis HCS Assay	Thermo Fisher Scientific	Catalog number C10289
Hoechst 33342	Thermo Fisher Scientific	Catalog number 62249
Starting Kit: Magnetic Plate + NeuroMag 200 μL	OZ Bioscience	Catalog number KC30800
AlphaScreen HA (Hemagglutinin) Detection Kit	PerkinElmer	Catalog number 6760612C
TruSeq Stranded mRNA Library Prep	Illumina	Catalog number 20020594
TruSeq Targeted RNA Custom Panel Kit	Illumina	Catalog number RT-101-1001
QuantSeq 3′ mRNA-Seq Library Prep Kit REV	Lexogen	Catalog number 016.24
iScriptcDNA synthesis kit	Biorad	Catalog number 1708891
KAPA SYBR FAST Universal 2X qPCR Master Mix	Kapa Biosystems	Catalog number KK4601 – 07959389001
Deposited Data
Raw Imaging files	This study, Mendeley Data	https://doi.org/10.17632/p34w7w78hy.1
Sequence files	This study, GEO GSE115490	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115490
Reference mouse genome annotation Gencode M6	Gencode	https://www.gencodegenes.org/mouse_releases/6.html
Experimental Models: Cell Lines
H. sapiens: HEK293T	Quattrone A. Lab (CIBIO)	RRID: CVCL_0045
M. musculus: NSC34	Tebu-bio	RRID: CVCL_D356
M. musculus: NSC-34-Trex	This study	N/A
M. musculus: NSC-34-HuD	This study	N/A
M. musculus: NSC-34-shHuD	This study	N/A
R. norvegicus: PC12	Quattrone A.Lab (CIBIO)	RRID: CVCL_0481
M. musculus: 46C ES	Conti L. Lab (CIBIO)	RRID: CVCL_Y482
H. sapiens: CRISPR Knockout Ro60 ES2, Clone 1	Huettelmaier S. Lab	N/A
H. sapiens: CRISPR Knockout Ro60 ES2, Clone 1	Huettelmaier S. Lab	N/A
Experimental Models: Organisms/Strains
C57BL/6J mice	The Jackson Laboratory	Catalog number 000664; RRID: IMSR_JAX:000664
Oligonucleotides
See Table S2 for complete list of primers used for qPCR analysis and barcodes used for CRAC	This study	N/A
Y3 siRNA AACUAAUUGAUCACAACCAGU	Köhn et al., 2015	N/A
Ctrl siRNA AGGUAGUGUAAUCGCCUUG	This study	N/A
HuD siRNA	Santa Cruz Biotechnology	Catalog number sc-37836
Control siRNA	Santa Cruz Biotechnology	Catalog number sc-37007
Y1 Northern Blot probe, ATAACTCACTACCTTCGGA CCAGCC	Köhn et al., 2015	N/A
Y3 Northern Blot probe, CTGTAACTGGTTGTGATCA ATTAGT	Köhn et al., 2015	N/A
Biotinylated ARE RNA AUUAUUUAUUAUUUAUUUA UUAUUUA	This study	N/A
Biotinylated mY1 RNA, GGCTGGTCCGAAGGTAGTG AGTTATCTCAATTGATTGTTCACAGTCAGTTACAGAT TGAACTCCTGTTCTACACTTTCCCCCCTTCTCACTA CTGCACTTGACTAGTCTTTT	Köhn et al., 2015	N/A
Biotinylated mY3 RNA, GGTTGGTCCGAGAGTAGTG GTGTTTACAACTAATTGATCACAACCAGTTACAGAT TTCTTTGTTCCTTCTCCGCTCCCACTGCTTCACTT GACCAGCCTTTT	Köhn et al., 2015	N/A
Biotinylated hY4 RNA, GGCTGGTCCGATGGTAGTG GGTTATCAGAACTTATTAACATTAGTGTCACTAAAG TTGGTATACAACCCCCCACTGCTAAATTTGACTG GCTTTTT	Köhn et al., 2015	N/A
Recombinant DNA
pCMV6-AN-His-HA	Origene	Catalog number PS100017
pCMV6-His-HA-HuD	This study	N/A
pCMV6-His-HA-HuD (R248K)	This study	N/A
pLenti CMV/TO His-HA-HuD	This study	N/A
pGEM-T-Y3wt	Köhn et al., 2015	N/A
pGEM-T-Y3mut (mutant lacking the HuD binding motif)	This study	N/A
pT7-HuD-WT	Fukao et al., 2009	N/A
pT7-HuD-MUT(mutant lacking any RNA-binding activity	Fukao et al., 2009	N/A
pT7-HuD-14-302	Fukao et al., 2009	N/A
pT7-HuD-216-385	Fukao et al., 2009	N/A
pIS1-Eef25UTR-TOPwt	Thoreen et al., 2012, A	Addgene Plasmid, Catalog number 38235
pIS1-Eef25UTR-TOPmut	Thoreen et al., 2012, A	Addgene Plasmid, Catalog number 38236
pIS1-Eef25UTR-TOPwt-3′UTR Eef1a1	This study	N/A
pIS1-Eef25UTR-TOPmut-3′UTR Eif4a3	This study	N/A
pIS1-Eef25UTR-TOPwt-3′UTR Eef1a1	This study	N/A
pIS1-Eef25UTR-TOPmut-3′UTR Eif4a3	This study	N/A
pHuD-GFP vector	Fallini et al., 2011	N/A
pshHuD	This study	N/A
pshY3	This study	N/A
pCDNA-SBP-HuD	This study	N/A
Software and Algorithms
Prism	GraphPad, v5	https://www.graphpad.com/
Harmony software version 4.1	PerkinElmer	N/A
ImageJ software version 1.43u	NIH	https://imagej.nih.gov/ij/
Microscope Software Zen 2012 (Blue Edition)	Zeiss	https://www.zeiss.com/
Adobe Photoshop 7.0	Adobe Systems Incorporated	https://www.adobe.com/products/photoshop.html
hyb	https://github.com/gkudla/hyb	N/A
Tophat (version 2.0.14)	http://ccb.jhu.edu/software/tophat/index.shtml	N/A
R	https://www.r-project.org/	N/A
STAR (version 2.5.3a)	https://github.com/alexdobin/STAR	N/A
Bioconductor	https://www.bioconductor.org/	N/A
enrichR	http://amp.pharm.mssm.edu/Enrichr/	N/A
Other
Stratalinker UV crosslinker 1800	Stratagene	N/A
UA-6 UV/VIS detector	Teledyne Isco	N/A
High Content Screening System Operetta	PerkinElmer	N/A