Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-Albumin | Cell Signaling Technology | Cat# 4929; RRID: AB_2225785 |
| Rat monoclonal anti-CD68 | Abcam | Cat# ab53444; RRID: AB_869007 |
| Chicken polyclonal anti-GFP | Abcam | Cat# ab13970; RRID: AB_300798 |
| Mouse monoclonal anti-Superoxide dismutase 3 | Abcam | Cat# ab80946; RRID: AB_1641091 |
| Rabbit monoclonal anti-Superoxide dismutase 3 | Abcam | Cat# ab171738 |
| Rabbit monoclonal anti-Vinculin | Cell Signaling Technology | Cat# 13901; RRID: AB_2728768 |
| Anti-rabbit IgG, HRP-linked antibody | Cell Signaling Technology | Cat# 7074; RRID: AB_2099233 |
| Anti-mouse IgG, HRP-linked antibody | Cell Signaling Technology | Cat#7076; RRID: AB_330924 |
| Hoechst 33342, Trihydrochloride, Trihydrate | Thermo Fisher Scientific | Cat# H3570 |
| Bacterial and virus strains | ||
| AAV2/5-CMV-hrGFP-hGH | Boston Children’s Hospital viral core, IDDRC | N/A |
| AAV2/5-CMV-hSOD3-hrGFP-hGH | Boston Children’s Hospital viral core, IDDRC | N/A |
| Biological samples | ||
| Human CSF | Table S1 and S2 | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Methotrexate disodium salt | Fisher Scientific | Cat# AAJ66364MD |
| Methotrexate hydrate | Sigma-Aldrich | Cat# M8407; CAS: 133073-73-1 |
| Methotrexate, fluorescein, triammonium salt | Thermo Fisher Scientific | Cat# M1198MP |
| 7-amino-actinomycin D (7AAD) | Biolegend | Cat# 420404 |
| MitoTracker deep red FM | Thermo Fisher Scientific | Cat# M22426 |
| CellROX deep red | Thermo Fisher Scientific | Cat# C10422 |
| Neurobasal medium, minus phenol red | GIBCO | Cat# 12348017 |
| Neurobasal-A | Life Technologies | Cat# 10888-022 |
| Basal Medium Eagle | GIBCO | Cat# 21010-046 |
| DMEM/F12 with glutamax | Life Technologies | Cat# 10565-018 |
| Penicillin/Streptomycin (10,000U/mL) | Life Technologies | Cat# 15140-122 |
| L-Glutamine | GIBCO | Cat# 25030081 |
| Glutamax | Life Technologies | Cat# 35050-061 |
| Glucose | Sigma Aldrich | Cat# G8769 |
| NaHCO3 | Sigma Aldrich | Cat# S5761 |
| Transferrin | Sigma Aldrich | Cat# T3309 |
| N2 | Life Technologies | Cat# 17502-048 |
| B27 | Life Technologies | Cat# 35050-044 |
| Doxycycline | Millipore | Cat# 324385 |
| BDNF | Peprotech | Cat# 450-02 |
| NT3 | Peptrotech | Cat# 450-03 |
| Laminin | ThermoFisher | Cat# 23017-015 |
| Non-essential amino acids | Life Technologies | Cat# 11140-050 |
| Puromycin | InVivogGen | Cat# ant-pr-1 |
| 10X HBSS | GIBCO | Cat# 14180-020 |
| 1X PBS | GIBCO | Cat# 10010023 |
| Liberase TL | Roche | Cat# 5401020001 |
| Accutase | Innovative Cell Tech | Cat# AT 104-500 |
| DNAse I | Roche | Cat# 104159 |
| Trypsin | Worthington | Cat# 3703 |
| Calf serum | Hyclone | Cat# SH30072.03 |
| Goat serum | Jackson | Cat# 005000121; RRID: AB_2336990 |
| AraC, Cytosine 1-β-d-arabinofuranoside | Millipore Sigma | Cat# C1768; CAS: 147-94-4 |
| Polybrene | Sigma | Cat# TR-1003-5 |
| 96-well plate | Grenier | Cat# 655090 |
| Poly-ornithine | Sigma | Cat# P2533 |
| Poly-D-lysine | Millipore Sigma | Cat# P6407; CAS: 27964-99-4 |
| Geltrex | Life Technologies | Cat# A1413301 |
| Cell TAK | Corning | Cat# 354240 |
| Paraformaldehyde | Millipore Sigma | Cat# P6148; CAS: 30525-89-4 |
| OCT compound | Fisher Healthcare | Cat# 23730571 |
| Fluoromount-G | Fisher scientific | Cat# OB10001 |
| Triton X-100 | Millipore Sigma | Cat# T9284; CAS: 9036-19-5 |
| Taqman fast universal PCR master mix | Applied Biosystems | Cat# 4366072 |
| RIPA lysis and extraction buffer | Thermo Scientific | Cat# 89900 |
| Halt protease and phosphatase inhibitor cocktail | Thermo Scientific | Cat# 78400 |
| NuPAGE 4–12% Bis-Tris protein gels | Invitrogen | Cat# NP0336 |
| NuPAGE LDS sample buffer | Invitrogen | Cat# NP0007 |
| NuPAGE sample reducing agent | Invitrogen | Cat# NP0009 |
| GE healthcare Amersham ECL select | Fisher Scientific | Cat# 45-000-999 |
| Amersham hybond P membranes, PVDF | Millipore Sigma | Cat# GE10600029 |
| Metabolomics QreSS Standard 1 (labelled) | Cambridge Isotope Libraries | Item Number: MSK-QRESS1-1 |
| Metabolomics QreSS Standard 2 (labelled) | Cambridge Isotope Libraries | Item Number: MSK-QRESS2-1 |
| (+)- Sodium L-ascorbate | Sigma-Aldrich | CAS: 134-03-2 |
| Metabolomics Amino Acid Mix Standard (Labeled) | Cambridge Isotope Laboratories | Item Number: MSK-A2-1.2 |
| Glutathione (Peptide Purity 95%+) (GLYCINE-13C2, 98%+;15N, 96–99%) 90% + NET PEPTIDE CNLM-6245-HP-10 | Cambridge Isotope Laboratories, Inc. | CAS: #:NA, PSO #:19A-0320 |
| Aminopterin | Shircks Laboratories | Product no. 16. 330 |
| Ellman’s reagent | Sigma-Aldrich | CAS: 69-78-03 |
| Ammonium Carbonate (LCMS Grade) | Sigma-Aldrich | CAS: 506-87-6 |
| Ammonium Hydroxide Solution (LCMS Grade) | Honeywell / Fluka | Cat# 44273-100ML |
| Acetonitrile (LCMS Grade) | Fisher chemical | CAS: 75-05-8 |
| Water (LCMS Grade) | Fisher chemical | CAS: 7732-18-5 |
| Critical commercial assays | ||
| Methotrexate ELISA kit | Enzo life sciences | Cat# 142-0001 |
| Seahorse XF cell mito stress test kit | Agilent Technologies | Cat# 103015-100 |
| CyQUANT cell proliferation assay | Fisher Scientific | Cat# C7026 |
| Superoxide dismutase assay kit | Cayman chemical | Cat# 706002 |
| TBARS assay kit | Cayman chemical | Cat# 10009055 |
| Glutathione peroxidase assay kit | Cayman chemical | Cat# 703102 |
| RNeasy micro kit | Qiagen | Cat# 74004 |
| iScript cDNA synthesis kit | Bio-Rad | Cat# 1708891 |
| Deposited data | ||
| Raw metabolomics data | NIH common fund’s national metabolomics data repository (NMDR) | https://www.metabolomicsworkbench.org/databases/metabolitedatabase.php |
| Anti-oxidative metabolism measurement in CSF of mice by quantitative LC/MS method to analyze effect of MTX on level of antioxidants in mouse controls 0–48hrs in CSF and hippocampus. | NIH common fund’s national metabolomics data repository (NMDR) | ST001974 |
| Anti-oxidation metabolism measurement in mouse CSF by quantitative LC/MS method to establish MTX effects on mouse metabolism in mouse controls 0–48hrs in CSF (repeat of 20200124 ChP-MTX-Anti-oxidative-study-test) | NIH common fund’s national metabolomics data repository (NMDR) | ST001975 |
| Anti-oxidative metabolism measurement in mouse CSF by quantitative LC/MS method of mouse CSF at 24H of MTX treatment, for either control GFP or SOD3-overexpressing ChP mice. | NIH common fund’s national metabolomics data repository (NMDR) | ST001976 |
| Anti-oxidation metabolism measurement in mammalian cells and tissues by quantitative LC/MS method of human patient/lymphoma patient CSF. | NIH common fund’s national metabolomics data repository (NMDR) | ST001977 |
| Anti-oxidation metabolism measurement in human patient CSF by quantitative LC/MS method. | NIH common fund’s national metabolomics data repository (NMDR) | ST001978 |
| Anti-oxidation metabolism measurement in mouse CSF by quantitative LC/MS method. | NIH common fund’s national metabolomics data repository (NMDR) | ST001979 |
| Experimental models: Cell lines | ||
| Primary rat cerebellar granule neurons | Lehtinen et al., 2006 | N/A |
| Human iPSC-derived cortical neurons | Boston Children’s Hospital Human Neuron Core | N/A |
| Experimental models: Organisms/strains | ||
| Rat: Sprague Dawley | Charles River Laboratories | Cat# 400 |
| Mouse: CD-1 | Charles River Laboratories | Cat# 022 |
| Mouse: CX3CR-1GFP | The Jackson Laboratory | Cat# 005582; RRID:IMSR_JAX:005582 |
| Oligonucleotides | ||
| Eukaryotic 18s rRNA endogenous control (VIC-MGB probe) | Thermo Fisher Scientific | Cat# 4319413E |
| Mouse SOD3 (FAM-MGB, Assay ID: Mm01213380_s1) | Thermo Fisher Scientific | Cat# 4453320 |
| Human SOD1 (FAM-MGB, Assay ID: Hs00533490_m1) | Thermo Fisher Scientific | Cat# 4331182 |
| Human SOD2 (FAM-MGB, Assay ID: Hs00167309_m1) | Thermo Fisher Scientific | Cat# 4331182 |
| Human SOD3 (FAM-MGB, Assay ID: Hs04973910_s1) | Thermo Fisher Scientific | Cat# 4453320 |
| Recombinant DNA | ||
| pAAV-IRES-HrGFP | Agilent Technologies | Cat# 240075 |
| pcDNA3.1-myc HisA (−) human SOD3 | Ota et al., 2016 | N/A |
| Software and algorithms | ||
| ImageJ | NIH | https://imagej.nih.gov/ij/, RRID: SCR_002285 |
| Zen | Zeiss | http://www.zeiss.com |
| ArrayScan XTI | ThermoFisher Scientific | http://assets.thermofisher.com |
| FlowJo software 10.6 | BD Biosciences | http://www.bdbiosciences.com |
| Wave software 2.6 | Agilent Technologies | http://www.agilent.com |
| GraphPad prism 7.04 | GraphPad | https://www.graphpad.com/scientific-software/prism/; GraphPad Prism, RRID: SCR_002798 |
| Tracefinder Peak Analysis Software | ThermoFisher | Cat# OPTON-31001 |
| Xcalibur Software | ThermoFisher | Cat# OPTON-30965 |
| Other | ||
| Agilent seahorse XFe96 analyzer | Agilent Technologies | http://www.agilent.com |
| Pellet pestle cordless motor homogenizer | Fisher Scientific | Cat# 12-141-362 |
| EMD Millipore ZIC-HILIC (100 × 2.1 mm, 3.5 um) | EMD Millipore | Cat# 150441 |
| Thermo Q Exactive Orbitrap Plus (Mass Spectrometer) | ThermoFisher | Cat# IQLAAEGAAPFALGMBDK |
| Vanquish HPLC System | ThermoFisher | Model # VF-P10-A |