| Antibodies |
|
|
| Rabbit polyclonal anti-G3BP1 |
MBL International |
Cat#RN048PW, RRID:AB_10794608 |
| Mouse monoclonal anti-G3BP1 |
EMD Millipore |
Cat#05-1938, RRID:AB_10561767 |
| Goat polyclonal anti-TIA1 |
Santa Cruz Biotech |
Cat#sc-1751, RRID:AB_2201433 |
| Rabbit polyclonal anti-TARDBP |
Abnova |
Cat#H00023435-A01, RRID:AB_461752 |
| Mouse monoclonal anti-VBP1 |
Origene |
Cat#UM500063, RRID:AB_2629076 |
| Rabbit polyclonal anti-GABARAPL2 |
Genetex |
Cat#GTX102006, RRID:AB_1240874 |
| Rabbit polyclonal anti-USP11 |
Bethyl |
Cat#A301-613A, RRID:AB_1211380 |
| Rabbit polyclonal anti-PPIG |
Bethyl |
Cat#A302-075A, RRID:AB_1604291 |
| Mouse monoclonal anti-Nestin |
EMD Millipore |
Cat#MAB5326, RRID:AB_2251134 |
| 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_10690651 |
| 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 |
| Thapsigargin |
Tocris |
Cat#1138 |
| Deposited Data |
|
|
| Quantitative MS data |
This paper |
MassIVE repository (https://massive.ucsd.edu) accession MSV000081554 |
| SG core proteome dataset |
(Jain et al., 2016) |
N/A |
| Protein-protein interaction datasets for ATXN2, C9orf72 DPRs, FUS, OPTN, TDP-43 and UBQLN2 |
(Blokhuis et al., 2016) |
N/A |
| Protein-protein interaction datasets for TDP-43 |
(Freibaum et al., 2010) |
N/A |
| Protein-protein interaction datasets for GR dipeptide repeats |
(Lee et al., 2016) |
N/A |
| Protein-protein interaction datasets for GR dipeptide repeatsPR dipeptide repeats |
(Lin et al., 2016) |
N/A |
| Human proteins with prion-like domains |
(March et al., 2016) |
N/A |
| Proteins co-precipitated with biotinylated isoxazole |
(Kato et al., 2012) |
N/A |
| Experimental Models: Cell Lines |
|
|
| Human Lenti-X 293T cells |
Clontech |
Cat#632180 |
| Human HepG2 cells |
ENCODE Project |
N/A |
| Human HeLa-S3 cells |
Lécuyer Lab |
N/A |
| HEK293T G3BP1-APEX2-GFP |
This paper |
N/A |
| HEK293T hPGK-APEX2-GFP |
This paper |
N/A |
| CV-B iPSCs |
(Gore et al., 2011) |
N/A |
| CV-B G3BP1-APEX2-GFP |
This paper |
N/A |
| hnRNPA2/B1 D290V-1.1 hiPSC |
Generated in-house (Martinez et al., 2016) |
N/A |
| hnRNPA2/B1 D290V-1.2 hiPSC |
Generated in-house, (Martinez et al., 2016) |
N/A |
| C9-3.2 G4C2 repeat-expansion hiPSC |
Generated in-house, fibroblasts described in (Lagier-Tourenne et al., 2013) |
N/A |
| C9-5.2 G4C2 repeat-expansion hiPSC |
Generated in-house, fibroblasts described in (Lagier-Tourenne et al., 2013) |
N/A |
| C9-6.3 G4C2 repeat-expansion hiPSC |
Generated in-house, fibroblasts described in (Lagier-Tourenne et al., 2013) |
N/A |
| Experimental Models: Organisms/Strains |
|
|
|
D. melanogaster: strain w[1118] |
Gao Lab |
N/A |
|
D. melanogaster: UAS-GFP strain |
Gao Lab |
N/A |
|
D. melanogaster: UAS-(GR)80 transgenic strain: Vg-Gal4/Cyo; UAS-(GR)80/TM6B
|
(Yang et al., 2015) |
N/A |
|
D. melanogaster: Mutant allele of Bel/DDX3X/Y |
Bloomington Drosophila Stock Center |
BDSC:19945; Flybase: FBst0019945 |
| y[1] w[67c23]; P{w[+mC] y[+mDint2] = EPgy2}bel[EY08943] |
|
D. melanogaster: RNAi of Bel/DDX3X/Y |
Bloomington Drosophila Stock Center |
BDSC:28049; Flybase: FBst0028049 |
| y[1] v[1]; P{y[+t7.7] v[+t1.8] = TRiP.JF02884}attP2 |
|
D. melanogaster: RNAi of Bel/DDX3X/Y |
Bloomington Drosophila Stock Center |
BDSC: 35302; Flybase: FBst0035302 |
| y[1] sc[*] v[1]; P{y[+t7.7] v[+t1.8] = TRiP.GL00205}attP2 |
|
D. melanogaster: |
Bloomington Drosophila Stock Center |
BDSC: 18765; Flybase: FBst0018765 |
| Mutant allele of Hrb27C/DAZAP1 |
| w[1118];PBac{w[+mC] = WH}Hrb27C[f04375]/CyO |
|
D. melanogaster: RNAi of Hrb27C/DAZAP1 |
Bloomington Drosophila Stock Center |
BDSC: 31684; Flybase: FBst0031684 |
| y[1] v[1]; P{y[+t7.7] v[+t1.8] = TRiP.JF01477}attP2 |
|
D. melanogaster: RNAi of Hrb27C/DAZAP1 |
Bloomington Drosophila Stock Center |
BDSC: 31685;Flybase: FBst0031685 |
| y[1] v[1]; P{y[+t7.7] v[+t1.8] = TRiP.JF01478}attP2 |
|
D. melanogaster: Mutant allele of Lig/UBAP2(L) |
Bloomington Drosophila Stock Center |
BDSC: 18242 ; Flybase: FBst0018242 |
| w[1118]; PBac{w[+mC] = RB}lig[e04268]/CyO |
|
D. melanogaster: Mutant allele of Lig/UBAP2(L) |
Bloomington Drosophila Stock Center |
BDSC: 14943; Flybase: FBst0014943 |
| y[1]; P{y[+mDint2] w[BR.E.BR] = SUPor-P}lig[KG08209]/CyO; ry[506] |
|
D. melanogaster: RNAi of Lig/UBAP2(L) |
Bloomington Drosophila Stock Center |
BDSC: 61857; Flybase: FBst0061857 |
| y[1] v[1]; P{y[+t7.7] v[+t1.8] = TRiP.HMJ23346}attP40 |
|
D. melanogaster: Mutant allele of Psi/FUBP1/3 |
Bloomington Drosophila Stock Center |
BDSC: 27192 ; Flybase: FBst0027192 |
| y[1] w[*]; P{w[+mC] = EP}Psi[G5862] |
|
D. melanogaster: RNAi of Psi/FUBP1/3 |
Bloomington Drosophila Stock Center |
BDSC:31301; Flybase: FBst0031301 |
| y[1] v[1]; P{y[+t7.7] v[+t1.8] = TRiP.JF01247}attP2 |
|
D. melanogaster: RNAi of Psi/FUBP1/3 |
Bloomington Drosophila Stock Center |
BDSC: 31683; Flybase: FBst0031683 |
| y[1] v[1]; P{y[+t7.7] v[+t1.8] = TRiP.JF01247}attP2 |
|
D. melanogaster: RNAi of Psi/FUBP1/3 |
Bloomington Drosophila Stock Center |
BDSC: 34825; Flybase: FBst0034825 |
| y[1] sc[*] v[1]; P{y[+t7.7] v[+t1.8] = TRiP.HMS00140}attP2 |
|
D. melanogaster: Mutant allele of Unr/CSDE1 |
Bloomington Drosophila Stock Center |
BDSC: 17673 ; Flybase: FBst0017673 |
| y[1] w[*]; P{w[+mC] = EP}Psi[G5862] |
|
D. melanogaster: Mutant allele of Unr/CSDE1 |
Bloomington Drosophila Stock Center |
BDSC: 10757 ; Flybase: FBst0010757 |
| w[1118]; PBac{w[+mC] = PB}Unr[c01923] |
|
D. melanogaster: RNAi of Unr/CSDE1 |
Bloomington Drosophila Stock Center |
BDSC: 32432; Flybase: FBst0032432 |
| y[1] sc[*] v[1]; P{y[+t7.7] v[+t1.8] = TRiP.HMS00428}attP2 |
|
D. melanogaster: RNAi of Unr/CSDE1 |
Bloomington Drosophila Stock Center |
BDSC: 29334; Flybase: FBst0029334 |
| y[1] v[1]; P{y[+t7.7] v[+t1.8] = TRiP.JF02496}attP2 |
|
D. melanogaster: GMR-GAL4/CyO, tub-GAL80; UAS-FUS-hR521C/TM6B, Tb
|
(Periz et al., 2015) |
N/A |
| D. melanogaster: GMR-GAL4, UAS-TDP-43-hM337V/CyO, tub-GAL80 |
(Periz et al., 2015) |
N/A |
| D. melanogaster: Rox8e04432 |
Exelixis Collectiion at Harvard University |
PBac{RB}Rox8e04432; Flybase: FBst1015699 |
| D. melanogaster: Rbp6d08411 |
Exelixis Collectiion at Harvard University |
P{XP}Rbp6d08411; Flybase: FBst1011661 |
| D. melanogaster: ligf03269 |
Exelixis Collectiion at Harvard University |
PBac{WH}ligf03269; Flybase: FBst1018357 |
| D. melanogaster: CG2889d07154 |
Exelixis Collectiion at Harvard University |
P{XP}CG2889d07154 mapped internally; Flybase: FBst1011297 |
| D. melanogaster: D12e01238 |
Exelixis Collectiion at Harvard University |
PBac{RB} D12e01238: mapped internally; Harvard Only |
| D. melanogaster: Su(var)205c06825 |
Exelixis Collectiion at Harvard University |
PBac{PB}Su(var)205c06825; Flybase: FBst1008382 |
| D. melanogaster: shepd07053 |
Exelixis Collectiion at Harvard University |
P{XP}shepd07053; Flybase: FBst1011268 |
| Oligonucleotides |
|
|
| Oligos for PCR, cloning and siRNA, see Table S8
|
This paper |
N/A |
| Recombinant DNA |
|
|
| Plasmid: pcDNA3 APEX2-NES |
(Lam et al., 2015) |
Addgene #49386 |
| Plasmid: GFP-Fusion HR Targeting Vector |
System Biosciences (SBI) |
Cat#HR120PA-1 |
| Plasmid: HR_G3BP1-V5-APEX2-GFP |
This study |
N/A |
| Plasmid: hPGK_V5-APEX2-GFP |
This study |
N/A |
| Plasmid: pSpCas9(BB)-2A-GFP (PX458) |
Gift from Feng Zhang (Ran et al., 2013) |
Addgene #48138 |
| Plasmid: pLIX403_UBAP2L_mCherry |
This study |
N/A |
| Plasmid: pLIX403_DUBA_UBAP2L_mCherry |
This study |
N/A |
| Plasmid: pRSV-Rev |
Gift from Didier Trono (Dull et al., 1998) |
Addgene #12253 |
| Plasmid: pMDLg/pRRE |
Gift from Didier Trono (Dull et al., 1998) |
Addgene #12251 |
| Plasmid: pCMV-VSV-G |
Gift from Bob Weinberg (Stewart et al., 2003) |
Addgene #8454 |
| Software and Algorithms |
|
|
| Enrichr Gene Set Enrichment Analysis |
(Kuleshov et al., 2016) |
http://amp.pharm.mssm.edu/Enrichr/ |
| Cytoscape |
(Shannon et al., 2003) |
http://www.cytoscape.org |
| Detecting significant changes in protein abundance |
(Kammers et al., 2015) |
http://www.biostat.jhsph.edu/~kkammers/software/eupa/R_guide.html |
