KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| (mouse) anti-Tdp-43 | Ling Shuo-Chien | FL4 |
| (rabbit) anti-hnRNP-H | Bethyl Labs | A300-511A |
| normal mouse IgG | Santa Cruz | sc-20-25 |
| rabbit control IgG | Proteintech | 30000-0-AP |
| (rabbit) anti-DDX5 | Abcam | ab21696 |
| (rabbit) anti-FUS/TLS | Proteintech | 11570-1-AP |
| (goat) anti-TIA-1 | Santa Cruz | sc-1751 |
| (rabbit) anti-TDP-43 | Proteintech | 12892-1-AP |
| (goat) anti-hnRNP H | Santa Cruz | sc-10042 |
| (donkey) anti-mouse-HRP | Jackson Immuno | 715-035-150 |
| (donkey) anti-rabbit-HRP | Jackson Immuno | 711-035-152 |
| Streptavidin-HRP | Jackson Immuno | 016-030-084 |
| (mouse) anti-TARDBP | Abnova | H00023435-M01 |
| (rabbit) anti-TDP-43 phosph-S409/410 | Lab of Leonard Petrucelli | |
| (rabbit) anti-DDX1 | ProteinTech | 11357-1-AP |
| (rabbit) anti-ILF3 | Bethyl Labs | NF90/NF110 Antibody, A303-121A |
| (rabbit) anti-U2AF2 | Novus Biologicals | NBP2-04138 |
| (rabbit) anti-Histone H3 | Abcam | ab18521 |
| (chicken) anti-MAP2 | Aves | MAP2 |
| (chicken) anti-NeuN | EMD | ABN91 |
| Anti-TARDBP | Santa Cruz | Cat# sc-376532 |
| Anti-MTDH (LYRIC) | Abcam | Cat# ab227981 |
| TMT10plex Isobaric Label Reagent Set plus TMT11-131C Label Reagent | Thermo Fisher | Cat# A34808 |
| Pierce™ Trypsin Protease, MS Grade | Thermo Fisher | Cat# 90057 |
| Sep-Pak C18 1 cc Vac Cartridge, 50 mg Sorbent per Cartridge, 55-105 μm Particle Size | Waters | Cat# WAT054955 |
| Thermo Scientific™ EASY-Spray™ HPLC Column | Thermo Fisher | Cat# ES805 |
| Bacterial and Virus Strains | ||
| DH5α competent cells | Thermo Fisher Scientific | Cat# 18255017 |
| E. coli NEB stable | New England Biolabs | Cat# C3040I |
| Biological Samples | ||
| Control fibroblast (code: pz2) | I IRCCS, Neurology and Laboratory of Neuroscience | Female; Mutation: none; age at biopsy-45 yrs; Healthy |
| Mutant TARDBP fibroblasts (code: A577 MF) | IRCCS, Neurology and Laboratory of Neuroscience | Male; Mutation TARDBP p.A382T; age at biopsy-56 yrs. |
| Chemicals, Peptides, and Recombinant Proteins | ||
| DL-Dithiothreitol | Millipore Sigma | Cat# D0632 |
| Iodoacetamide | Millipore Sigma | Cat# I6125 |
| Urea | Fisher | Cat# BP169 |
| PhosSTOP™ | Millipore Sigma | Cat# PHOSS-RO |
| cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail | Millipore Sigma | Cat# 11836170001 |
| Triethylammonium bicarbonate buffer | Millipore Sigma | Cat# T7408 |
| Formic Acid, 99.0+%, Optima™ LC/MS Grade, Fisher Chemical | Fisher | Cat# A117 |
| Acetonitrile, Optima™ LC/MS Grade, Fisher Chemical | Fisher | Cat# A955 |
| Ammonium Hydroxide, ACS Reagent Grade, 28.0-30.0% as NH3 | Fisher | Cat# RABA0020500 |
| Critical Commercial Assays | ||
| Pierce™ Quantitative Colorimetric Peptide Assay | Thermo Scientific | Cat# 23275 |
| Pierce™ BCA Protein Assay Kit | Thermo Scientific | Cat# 23225 |
| Deposited Data | ||
| Protein sequences | UniProt Consortium | PMID: 29425356 |
| Reference complexes | CORUM | PMID: 19884131 |
| Reference complexes | IntAct | PMID:24234451 |
| Reference complexes | GO | PMID: 10802651; PMID: 27899567 |
| Reference complexes | Metazoan | PMID: 26344197; PMID: 26870755 |
| Reference complexes | Human soluble | PMID: 22939629 |
| Functional evidence | Mouse Net v2.0 | PMID: 26527726 |
| Functional evidence | Human Subcellular localization | PMID:28495876 |
| Functional evidence | Cell type and brain region – Mouse brain Proteome | PMID:26523646 |
| Functional evidence | Allen Brain Atlas – Mouse brain | PMID: 17151600 |
| Functional evidence | RNA-Seq from SRA | PMID: 21062823 |
| Functional evidence | GeneCards | PMID: 27322403 |
| Protein abundances | PAXdb | PMID: 25656970 |
| Disease association | DisGenNET | PMID: 27924018 |
| Experimental PPIs | AP/MS, BF/MS, Y2H | PMID: 22939629; PMID: 26344197; PMID: 26496610; PMID: 28514442 |
| Gene expression | Sc-RNA-Seq | PMID: 30096314; PMID: 30096299 |
| RNA binding protein assignment | Census of RNA binding proteins | PMID: 25365966 |
| Functional PPIs | Human Net v2.0, Mouse Net v.2 | PMID: 30418591; PMID: 26527726 |
| Domains and Orthologues | PhyloPro 2.0 | PMID: 26980519 |
| RNA-Seq database | Gene expression Omnibus | PMID: 27008011 |
| De novo variants | denovo-db v.1.5 | PMID: 27907889 |
| Autism genes | SFARI (Mar 5, 2018) | PMID: 19015121 |
| Population variants | NHLBI ESP exome-sequencing study | PMID: 23201682 |
| Protein interaction interface | Interactome INSIDER | PMID: 29355848 |
| Mouse to human gene mapping | Ensemble 92 | PMID: 29155950 |
| Human PPI databases | Inweb3, InWeb_IM | PMID: 17344885, PMID: 27892958 |
| Human prenatal gene expression | BrainSpan | PMID: 24695229 |
| Schizophrenia risk genes | PMID: 25056061 | |
| Autism risk genes | PMID: 26402605 | |
| Developmental disorder associated genes | PMID: 28135719 | |
| Experimental Models: Cell Lines | ||
| SH-SY5Y | ATCC | CRL-2266 |
| Experimental Models: Organisms/Strains | ||
| CD1 wild type mice | ||
| C57BI/6J | JAX labs | 000664 |
| TDP-43WT/WT | JAX via AD. Gitler | 012836; B6;SJL-Tg(Thy1-TARDBP)4Singh/J |
| Atxn2[+/−] | JAX via AD. Gitler | 101043; B6129SF1/J |
| CamKCreER TDP-43 KO | Gift from P. Wong | Chiang et al., 2010. PMID: 20660762 |
| Oligonucleotides | ||
| siGENOME Human TARDBP | Dharmacon | siTDP, 23435 |
| siGENOME Human HNRNPH1 | Dharmacon | siH1, 3187 |
| siGENOME Human DDX5 | Dharmacon | siDDX5, 1655 |
| siGENOME Non-Targeting siRNA Pool #1 | Dharmacon | siCtrl |
| SORT1total_Ex15_F | Life Tech. | 5’-TCCATCTGCCTCTGTTCCCTG |
| SORT1total_Ex16_R | Life Tech. | 5‘-GGTGTTCTTCTCTTCCGTACAGACAA |
| SORT1WT_Ex17_F | Life Tech. | 5‘-TGGGGTAAATCCAGTTCGAG |
| SORT1WT_Ex17-18_R | Life Tech. | 5‘-GACTTGGAATTCTGTTTTTCCGGAC |
| SORT1+17b_Ex17b_F | Life Tech. | 5‘-AATCCAGCTCTGCCTCCTCT |
| SORT1+17b_Ex18_R | Life Tech. | 5‘-TCCCACGATGGCCAGGATAA |
| ACTB_931F | Life Tech. | 5‘-GACAGGATGCAGAAGGAGAT |
| ACTB_1011R | Life Tech. | 5‘-GTACTTGCGCTCAGGAGGA |
| TARDBP-outer_Forward | Millipore-Sigma | CAAGATGAGCCTTTGAGAAGC |
| TARDBP-outer_Reverse | Millipore-Sigma | AGAGCTGCCAGGAAACAGC |
| TARDBP-G287A_ Forward | Millipore-Sigma | AATCAGGCTGGATTTGGTAATAGCAGAGGG |
| TARDBP-G287A_ Reverse | Millipore-Sigma | AAATCCAGCCTGATTCCCAAAGC |
| TARDBP-A315T_ Forward | Millipore-Sigma | TTGGTACGTTCAGCATTAATCCAGCC |
| TARDBP-A315T_Reverse | Millipore-Sigma | GAACGTACCAAAGTTCATCCCACC |
| TARDBP-G368A_ Forward | Millipore-Sigma | GCCTTCGCTTCTGGAAATAACTCTTATAGTGG |
| TARDBP-G368A_ Reverse | Millipore-Sigma | CCAGAAGCGAAGGCCTGG |
| TARDBP-W385G_ Forward | Millipore-Sigma | AATTGGTGGCGGATCAGCATCCAATGC |
| TARDBP-W385G_ Reverse | Millipore-Sigma | ATCCGCCACCAATTGCTGCACC |
| Recombinant DNA | ||
| pENTR-TARDBP-G287A | ||
| pENTR-TARDBP-A315T | ||
| pENTR-TARDBP-G368A | ||
| pENTR-TARDBP-W385A | ||
| pLD-puro-Cc-TARDBP-WT-VA | ||
| pLD-puro-Cc-TARDBP-G287A-VA | ||
| pLD-puro-Cc-TARDBP-A315T-VA | ||
| pLD-puro-Cc-TARDBP-G368A-VA | ||
| pLD-puro-Cc-TARDBP-W387G-VA | ||
| Software and Algorithms | ||
| Sequence database searching | MaxQuant 1.5.5.1 & 1.6.0.16 | PMID: 19029910 |
| Ortholog mapping | InParanoid8 | PMID: 25429972 |
| PPI Prediction | EPIC | PMID: 31308550 |
| Complex prediction | ClusterONE | PMID: 22426491 |
| Network visualization | Cytoscape v. 3.5.1 | PMID: 14597658 |
| Gene Set Enrichment Analysis | GSEA | PMID: 16199517; PMID: 12808457 |
| Enrichment analysis | BinGO 3.0 Cytoscape App | PMID: 15972284 |
| Enrichment analysis | DAVID Bioinformatics resource 6.8 | PMID: 19131956 |
| Hierarchical clustering | Cluster 3.0 | PMID: 14871861 |
| Cluster visualization | Java TreeView v 1.1.6r4 | PMID: 15180930 |
| Hypergeometric test | R function | Stats: R package |
| RNA-Seq data analysis | R function | edgeR: R Package |
| RNA-SEQ analysis | StringTie | PMID:25690850 |
| RNA-SEQ analysis | HiSAT | PMID:25751142 |
| Binomial test | Scipy function | Python package |
| Mann-Whitney U test | Scipy function | Python package |
| Network analysis | NetworkX | Python package |
| PIPER | Schrödinger, LLC | Protein-protein docking |
| ITASSER | Protein structure and function prediction | PMID: 25549265 |
| Plots | R function | ggplot2: R package |
| Venn diagram | R function | VennDiagram: R package |
| Overlap analysis | Venn Draw Tool | http://bioinformatics.psb.ugent.be/webtools/Venn/ |
| Surrogate Variable Analysis | R function | sva: R package |
| Quantile Normalization | R function | preprocessCore: R package |
| Heatmap | R function | ComplexHeatmap: R package |
| R | R version 3.5 | R Foundation for Statistical Computing |
| IsobaricAnalyzer | C++ Library | OpenMS v2.4 |
| Other | ||
| Proteomics data deposition | PRIDE | PXD011304 |
| Proteomics data deposition | BioGRID | To be deposited |
| Nano-HPLC | Thermo Scientific | EASY-nLC™ 1200 System |
| HPLC | Agilent | Agilent 1100 Series |
| Mass Spectrometer | Thermo Scientific | Q Exactive™ HF-X Hybrid Quadrupole-Orbitrap™ Mass Spectrometer |