Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Chemical compound, drug | Phosphate Buffered Saline Tablet | Sigma | Cat# P4417-100TAB | |
| Chemical compound, drug | Methanol, Optima grade for LC/MS | Fisher Scientific | Cat# A456-4 | |
| Chemical compound, drug | Acetonitrile, Optima Grade for LCMS | Fisher Scientific | Cat# A955-4 | |
| Chemical compound, drug | MeOH, Optima Grade for LCMS | Fisher Scientific | Cat# A456-4 | |
| Chemical compound, drug | Water, Optima Grade for LCMS | Fisher Scientific | Cat# W6-4 | |
| Commercial assay, kit | LS magnetic enrichment columns | Miltenyi | Cat# 130-042-401 | |
| Commercial assay, kit | MidiMACS separator | Miltenyi | Cat# 130-042-301 | |
| Other | Plastic microfuge tube opener | USA Scientific | Cat# 1400–1508 | For minimizing metabolite contamination when opening microfuge tubes |
| Antibody | FITC anti-mouse B220, clone: RA3-6B2 (rat monoclonal) | Tonbo | Cat# 35–0452 U500, RRID:AB_2621690 | Dilution: 1:400 For bone marrow HSC isolation by flow cytometry |
| Antibody | FITC anti-mouse Gr-1, clone: RB6-8C5 (rat monoclonal) | Tonbo | Cat# 35–5931 U500, RRID:AB_2621721 | Dilution: 1:400 For bone marrow HSC isolation by flow cytometry |
| Antibody | FITC anti-mouse Terr119, clone: TER-119 (rat monoclonal) | Tonbo | Cat# 35–5921 U500, RRID:AB_2621720 | Dilution: 1:400 For bone marrow HSC isolation by flow cytometry |
| Antibody | FITC anti-mouse CD2, clone: RM2-5 (rat monoclonal) | Tonbo | Cat# 35–0021 T100, RRID:AB_2621657 | Dilution: 1:400 For bone marrow HSC isolation by flow cytometry |
| Antibody | FITC anti-mouse CD3, clone: 17A2 (rat monoclonal) | Tonbo | Cat# 35–0032 U100, RRID:AB_2621660 | Dilution: 1:400 For bone marrow HSC isolation by flow cytometry |
| Antibody | FITC anti-mouse CD5, clone: 53–7.3 (rat monoclonal) | Biolegend | Cat# 100606, RRID:AB_312735 | Dilution: 1:400 For bone marrow HSC isolation by flow cytometry |
| Antibody | FITC anti-mouse CD8α, clone: 53–6.7 (rat monoclonal) | Tonbo | Cat# 35–0081 U500, RRID:AB_2621671 | Dilution 1:400 For bone marrow HSC isolation by flow cytometry |
| Antibody | APC-e780 anti-mouse c-kit, clone: 2B8 (rat monoclonal) | eBiosciences | Cat# 47-1171-82, RRID:AB_1272177 | Dilution: 1:200 For bone marrow HSC isolation by flow cytometry |
| Antibody | PerCP-Cy5.5 anti-mouse Sca-1, clone: D7 (rat monoclonal) | BioLegend | Cat# 108124, RRID:AB_893615 | Dilution 1:200 |
| Antibody | APC anti-mouse CD48, clone: HM48-1 (Armenian hamster monoclonal) | eBiosciences | Cat# 17-0481-82, RRID:AB_469408 | Dilution 1:200 |
| Antibody | PE anti-mouse CD150, clone: TC15-12F12.2 (rat monoclonal) | BioLegend | Cat# 115904, RRID:AB_313683 | Dilution 1:200 |
| Antibody | APC anti-Mouse CD45, clone: 30-F11 (rat monoclonal) | Tonbo | Cat# 20–0451 U100, RRID:AB_2621573 | Dilution 1:100 |
| Antibody | APC anti-Mouse CD31 (PECAM-1), clone: 390 (rat monoclonal) | Biolegend | Cat# 102410, RRID:AB_312905 | Dilution 1:100 |
| Antibody | APC anti-Mouse Ter119, clone: Ter119 (rat monoclonal) | Tonbo | Cat# 20–5921 U100, RRID:AB_2621609 | Dilution 1:100 |
| Antibody | FITC anti-Human HLA-A, B, C, clone: G46-2.6 (mouse monoclonal) | BD Biosciences | Cat# 555552, RRID:AB_395935 | Dilution 1:20 |
| Antibody | Anti-Mouse c-Kit, conjugated to para-magnetic beads, clone: 3C11 (rat monoclonal) | Miltenyi | Cat# 130-091-224, RRID:AB_2753213 | (60 µl) 60 µl beads per3 × 108 whole bone marrow cells |
| Antibody | Anti-Mouse CD45, conjugated to para-magnetic beads, clone: 30-F11 (rat monoclonal) | Miltenyi | Cat# 130-052-301, RRID:AB_2877061 | (3 µl) 3 µl beads per1 × 106 whole bone marrow cells |
| Chemical compound, drug | DAPI | Sigma-Aldrich | Cat# D8417-10mg | 1 µg/ml for flow cytometry |
| Cell line | Human – HNT-34 AML cell line | Provided by Jian Xu’s Laboratory at Children’s Research Institute at UT Southwestern Medical Center. Original source: DSMZ | ACC 600, RRID: CVCL_2071 | |
| Cell line | Human DND-41 cell line | Provided by Jian Xu’s Laboratory at Children’s Research Institute at UT Southwestern Medical Center. Original source: Hui Feng, M.D./Ph.D.; Boston University |
RRID: CVCL_2022 | |
| Cell line | Human melanoma xenograft M405 | Sci Trans Med 4:159ra PMCID:PMC4501487 |
M405 | |
| Strain, strain background | NOD.CB17-Prkdcscid Il2rgtm1Wjl/Szj (NSG) mice | Jackson laboratories | 005557, RRID:IMSR_JAX:005557 | |
| Strain, strain background | C57BL/Ka Thy1.1 mice | Derived from Henry Kaplan’s laboratory at Stanford University | N/A | |
| Other | ZIC-pHILIC column (2.1 × 150, 5 μm) | Millipore Sigma | Cat# 1504600001 | |
| Software, algorithm | Omics Data Analyzer (ODA) | This manuscript | https://git.biohpc.swmed.edu/CRI/ODA | See Materials and methods, section ‘Statistical analysis of metabolomics data’ |
| Software, algorithm | Graphpad Prism V8.3 | Graphpad | RRID:SCR_002798 | |
| Software, algorithm | FlowJo V10.7.1 | BD Biosciences | RRID:SCR_008520 | |
| Software, algorithm | Freestyle V1.5 | Thermo Scientific | N/A | |
| Software, algorithm | Trace Finder V4.0 | Thermo Scientific | N/A | |
| Software, algorithm | Compound Discoverer V3.1 | Thermo Scientific | N/A | |
| Chemical compound, drug | Formic Acid Optima | Fisher | Cat# A11750 | |
| Chemical compound, drug | Ammonium acetate, Optima | Fisher | Cat# A11450 | |
| Chemical compound, drug | Ammonium hydroxide, Optima | Fisher scientific | Cat# A470-250 | |
| Chemical compound, drug | Methotrexate | Selleck Chem | Cat# S1210 | |
| Chemical compound, drug | SplashMix | Avanti | Cat# 330707 |