REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Antibodies | ||
Rabbit anti-G3BP1 | Thermo Fisher Scientific | Cat#PA5-29455; RRID:AB_2546931 |
Goat anti-eIF3η | Santa Cruz Biotechnology | Cat#N-20; RRID:AB_671941 |
Donkey anti-goat 647 | Invitrogen | Cat#A21447; RRID:AB_141844 |
Donkey anti-rabbit 488 | Invitrogen | Cat#A21206; RRID:AB_2535792 |
Rabbit anti-phospho-G3BP1 (pS149) | Sigma Aldrich | Cat#G8046; RRID:AB_1840867 |
Mouse anti-puromycin (clone 12D10) | Merck Millipore | Cat#MABE343; RRID:AB_2566826 |
Rabbit anti-eIF2a(Ser52) | Thermo Fisher Scientific | Cat#44-728G; RRID:AB_2533736 |
Mouse anti-eIF2a | Santa Cruz Biotechnology | Cat#sc-133132; RRID:AB_1562699 |
Goat anti-EGFP | In house | N/A |
Bacterial and Virus Strains | ||
BL21-AI One Shot Chemically Competent E. coli | Thermo Fisher Scientific | Cat#607003 |
Chemicals, Peptides and Recombinant Proteins | ||
Ubc9WT-6xHis | Mateju et al., 2017 | O-3299 |
Ubc9ts-6xHis | Mateju et al., 2017 | O-3298 |
GFP-G3BP1(WT) | This paper | L-515 |
GFP-G3BP1(ΔNTF2) | This paper | TH1321 |
GFP-G3BP1(ΔRG) | This paper | TH0999 |
GFP-G3BP1(ΔE1) | This paper | L-663 |
GFP-G3BP1(ΔE2) | This paper | L-664 |
GFP-G3BP1(ΔE1ΔE2) | This paper | L-667 |
GFP-G3BP1(S149A) | This paper | L-548 |
GFP-G3BP1(S149E) | This paper | L-549 |
GFP-G3BP1(S149A/S232A) | This paper | L-686 |
SNAP-G3BP1(WT) | This paper | L-587 |
mCherry-Caprin1 | This paper | TH1232 |
GFP-G3BP2(WT) | This paper | TH1434 |
GFP | This paper | D292 |
GFP-hnRNPA1L | Wang et al., 2018 | TH1261 |
GFP-hnRNPA2B1 | Wang et al., 2018 | TH1252 |
FUS-GFP | Wang et al., 2018 | TH1204 |
TDP43-GFP | Wang et al., 2018 | TH1083 |
GFP-hnRNPA1L2 | Wang et al., 2018 | TH1275 |
GFP-hnRNPA0 | Wang et al., 2018 | TH1250 |
GFP-hnRNPAB | Wang et al., 2018 | TH1251 |
GFP-hnRNPA1S | Wang et al., 2018 | TH1164 |
GFP-hnRNPDL | Wang et al., 2018 | TH1254 |
GFP-hnRNPA3 | Wang et al., 2018 | TH1202 |
GFP-TIAL1 | Wang et al., 2018 | TH1257 |
GFP-TIA1 | Wang et al., 2018 | TH1256 |
GFP-PSPC | This paper | TH1255 |
SFPQ-GFP | This paper | TH1263 |
RNaseOUT | Invitrogen | Cat#10777019 |
Nucleotides: ATP, CTP, GTP, and UTP | Roche | Cat#11277057001 |
DNase I | New England Biolabs | Cat#M0303S |
E. coli PolyA Polymerase | Thermo Fisher Scientific | Cat#AM1350 |
HCS CellMask Blue Stain | Invitrogen | Cat#H32720 |
Hoechst 33342, Trihydrochloride, Trihydrate – 10 mg/ml solution in water | Invitrogen | Cat#H3570 |
Blasticidin S HCl | Invitrogen | Cat#R21001 |
Lipofectamine 2000 | Life Technology | Cat#11668-019 |
Opti-MEM | GIBCO | Cat#31985062 |
DMEM, high glucose, GlutaMAX Supplement, pyruvate | GIBCO | Cat#31966021 |
DMEM, high glucose, no glutamine, no phenol red | GIBCO | Cat#31053028 |
cOmplete Protease Inhibitor Cocktail | Roche | Cat#11836145001 |
cOmplete, EDTA-free Protease Inhibitor Cocktail | Roche | Cat#05056489001 |
RNase A | PanReac AppliChem | Cat#A2760 |
Polyethylene glycol 20000 | Merck | Cat#817018 |
SNAP-Surface Alexa Fluor 546 | New England Biolabs | Cat#S9132S |
T4 RNA ligase 1 | New England Biolabs | Cat#M0204S |
pCp-Cy5 | Jena Bioscience | Cat#NU-1706-CY5 |
Lambda Protein Phosphatase | New England Biolabs | Cat#P0753S |
Nonidet P 40 | Sigma-Aldrich | Cat#74385 |
2-[Methoxy(polyethyleneoxy)propyl]trimethoxysilane; 90% 6-9 PE-units | Abcr GmbH | Cat#AB111226 |
Sodium hydrogen arsenate heptahydrate, ASC, 98.0-102.0% | Alfa Aesar | Cat#33373 |
Critical Commercial Assays | ||
RNeasy Mini Kit (50) | QIAGEN | Cat#74104 |
mMESSAGE mMACHINE T7 Transcription Kit | ThermoFisher | Cat#AM1344 |
Poly(A) Tailing Kit | ThermoFisher | Cat#AM1350 |
Microspin G-25 Columns | GE Healthcare | Cat#GE27-5325-01 |
Pierce™ Polyacrylamide Spin Desalting Columns, 7K MWCO | ThermoFisher | Cat#89849 |
Experimental Models: Cell Lines | ||
G3BP1(WT) BAC in HeLa Kyoto cell line | Mateju et al., 2017 | MCB_ky_7510 (C-terminal mCherry tag; FACS sorted) |
U2OS | Kedersha et al., 2016; Laboratory of Paul Anderson | N/A |
U2OS G3BP1/2 knock out cell line | Kedersha et al., 2016; Laboratory of Paul Anderson | N/A |
Sf9 cells | Expression Systems | Cat#94-001F |
Oligonucleotides | ||
polyA(60) RNA | This paper; Eurofins Genomics | N/A |
Poly(A) | Sigma-Aldrich | Cat#10108626001 |
Poly(C) | Sigma-Aldrich | Cat#P4903 |
Poly(G) | Sigma-Aldrich | Cat#P4404 |
Poly(U) | Sigma-Aldrich | Cat#P9528 |
Human spinal cord poly(A)+ RNA | Clontech | Cat#636142 |
NEAT1 RNA | This paper | N/A |
5-loop RNA | This paper | N/A |
Ribosomal RNA | Bioworld | Cat#11020001-2 |
Recombinant DNA | ||
pCRII-TOPO-hNEAT1 | Clemson et al., 2009; Laboratory of Archa Fox | Addgene Plasmid #61518 |
pSCA-5loopPlus5 | This paper | L-480 |
Software and Algorithms | ||
Fiji | NIH | https://fiji.sc/ |
NCPR | Alan Bleasby European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK | http://www.bioinformatics.nl/cgi-bin/emboss/charge |
PLAAC | Lancaster et al., 2014 | http://plaac.wi.mit.edu/ |
IUPred | Dosztányi et al., 2005 | https://iupred2a.elte.hu |
KNIME | KNIME.com AG | https://www.knime.com |
R / RStudio | R Core Team |
https://www.r-project.org/ https://www.rstudio.com/ |