KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
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| Antibodies | ||
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| Hamster monoclonal anti-mouse TNF-α | eBioscience | Cat # 14-7423-81; RRID: AB_2721314 |
| Rabbit polyclonal biotinylated anti-mouse TNF-α | eBioscience | Cat# 13-7341-81; RRID: AB_466950 |
| Rat monoclonal anti-mouse IL-6 | eBioscience | Cat# 14-7061-81; RRID: AB_468422 |
| Rat monoclonal biotinylated anti-mouse IL-6 | BioLegend | Cat# 504601; RRID: AB_2127458 |
| Hamster monoclonal anti-mouse IL-1β | eBioscience | Cat# 14-7012-81; RRID: AB_468396 |
| Rabbit polyclonal anti-mouse IL-1β | eBioscience | Cat# 13-7112-81; RRID: AB_466924 |
| Rat monoclonal anti-mouse IL-6, PerCP-eFluor 710 | Invitrogen | Cat# 46-7061-82; RRID: AB_2573829 |
| Rat monoclonal anti-mouse TNF-α, PE-efluor 610 | Invitrogen | Cat# 61-7321-82; RRID: AB_2574666 |
| Rat monoclonal anti-mouse IL-1β, PE-Cy7 | Invitrogen | Cat# 25-7114-82; RRID: AB_2573526 |
| Rat monoclonal anti-mouse iNOS, Alexa Fluor 700 | Invitrogen | Cat# 56-5920-80; RRID: AB_2848473 |
| Rat monoclonal anti-mouse F4/80, Super Bright 780 | Invitrogen | Cat# 78-4801-82; RRID: AB_2802477 |
| Mouse monoclonal anti-mouse CD64 (FcγRI), APC | BioLegend | Cat# 139305; RRID: AB_11219205 |
| Rat monoclonal anti-mouse CD11b, Super Bright 645 | Invitrogen | Cat# 64-0112-82; RRID: AB_2662387 |
| Rat monoclonal anti-mouse Ly6C, APC/Cyanine7 | BioLegend | Cat# 128025; RRID: AB_10643867 |
| Rat monoclonal anti-mouse MHC Class II (I-A), PE | Invitrogen | Cat# 12-5321-82; RRID: AB_465928 |
| Rat monoclonal anti-mouse CD45, Super Bright SB600 | Invitrogen | Cat# 63-0451-82; RRID: AB_2637149 |
| Mouse monoclonal anti-mouse NK1.1, Pacific Blue | BioLegend | Cat# 108721; RRID: AB_2234352 |
| Rat monoclonal anti-mouse Ly6G, Pacific Blue | BioLegend | Cat# 127611; RRID: AB_1877212 |
| Rat monoclonal anti-mouse TER119/Erythroid cells, Pacific Blue | BioLegend | Cat# 116231; RRID: AB_2149212 |
| Rat monoclonal anti-mouse CD3, Pacific Blue | BioLegend | Cat# 100213; RRID: AB_493644 |
| Rat monoclonal anti-mouse CD19, Pacific Blue | BioLegend | Cat# 115526; RRID: AB_493341 |
| Rabbit monoclonal anti-phospho-NF-kB p65 (Ser536) (93H1) | Cell Signaling Technology | Cat# 3033; RRID: AB_331284 |
| Rabbit anti-IκBα | Cell Signaling Technology | Cat# 9242; RRID: AB_331623 |
| Mouse monoclonal anti-phospho-IκBα (Ser32/36) (5A5) | Cell Signaling Technology | Cat# 9246; RRID: AB_2267145 |
| Mouse monoclonal anti-phospho-p38 MAPK (Thr180/Tyr182) (28B10) | Cell Signaling Technology | Cat# 9216; RRID: AB_331296 |
| Rabbit polyclonal anti-phospho-LDHA (Tyr10) | Cell Signaling Technology | Cat# 8176; RRID: AB_11220238 |
| Rabbit monoclonal anti-H3, acetyl (Lys27) (D5E4) XP | Cell Signaling Technology | Cat# 8173; RRID: AB_10949503 |
| Rabbit monoclonal anti-H3, acetyl (Lys18) (D8Z5H) | Cell Signaling Technology | Cat# 13998; RRID: AB_2783723 |
| Rabbit monoclonal anti-H3, acetyl (Lys14) (D4B9) | Cell Signaling Technology | Cat# 7627; RRID: AB_10839410 |
| Rabbit monoclonal anti-H3, acetyl (Lys9) (C5B11) | Cell Signaling Technology | Cat# 9649; RRID: AB_823528 |
| Rabbit monoclonal anti-H3, trimethyl (Lys27) (C36B11) | Cell Signaling Technology | Cat# 9733; RRID: AB_2616029 |
| Mouse monoclonal anti-α-tubulin (DM1A) | Cell Signaling Technology | Cat# 3873; RRID: AB_1904178 |
| Rabbit recombinant monoclonal anti-L-lactyl lysine | PTM BIO | Cat# PTM-1401RM; RRID: AB_2942013 |
| Rabbit recombinant monoclonal anti-H3, lactyl (Lys18) | PTM BIO | Cat# PTM-1406RM; RRID: AB_2909438 |
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| Chemicals, peptides, and recombinant proteins | ||
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| Lipopolysaccharides from Escherichia coli O26:B6 | Sigma | L3755 |
| L-(+)-Lactic acid | Sigma | L6402 |
| ATP | Sigma | A6419 |
| L-Lactic acid-13C3 | Sigma | 746258 |
| cyano-4-hydroxycinnamic acid | Sigma | S8612 |
| MDL-12,330A hydrochloride | Sigma | M182 |
| Trichostatin A | Sigma | T8552 |
| BMS-303141 | Sigma | SML0783 |
| DIM-C-pPhOH | Selleck Chemicals | S6799 |
| Recombinant mouse TNF-α | PeproTech | 315-01A |
| Recombinant mouse IL-6 | PeproTech | 216-16 |
| Recombinant mouse IL-1β | PeproTech | 211-11B |
| Recombinant mouse RELM-α | PeproTech | 450-26 |
| 2-deoxy-D-glucose | Cayman Chemical | 14325 |
| D-glucose-13C6 | Cambridge Isotope | CLM-1396 |
| BD GolgiPlug | Fisher Scientific | BDB555029 |
| BD Cytofix/Cytoperm solution | Fisher Scientific | BDB554714 |
| Lipofectamine RNAiMAX | Thermo Fisher Scientific | 13778030 |
| Cytosporone B | R&D Systems | 5459 |
| Dextran sulfate sodium (molecular mass 36–50 kDa) | MP Biomedicals | MFCD00081551 |
| Collagenase VIII | Sigma | C2139 |
| DNase I | ROCHE | 10104159001 |
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| Critical commercial assays | ||
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| Dual-Glo Luciferase Reporter Assay | Promega | E2920 |
| Prostaglandin E2 (PGE2) Parameter Assay Kit | R&D Systems | KGE004B |
| LIVE/DEAD Fixable Aqua Dead Cell Stain Kit | Thermo Fisher Scientific | L34965 |
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| Deposited data | ||
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| RNA-seq | This paper | GEO: GSE253050 |
| ATAC-seq | This paper | GEO: GSE253050 |
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| Experimental models: Cell lines | ||
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| RAW264.7 | American Type Culture Collection | TIB-71 |
| 293T | American Type Culture Collection | CRL-3216 |
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| Experimental models: Organisms/strains | ||
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| C57BL/6 mice | Jackson Laboratory | 000664 |
| C57BL/6NJ mice (control mice for Acod1−/− mice) | Jackson Laboratory | 005304 |
| Acod1−/− mice | Jackson Laboratory | 029340 |
| Nr4a1wt control mice | Jackson Laboratory | 100903 |
| Nr4a1−/− mice | Jackson Laboratory | 06187 |
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| Oligonucleotides | ||
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| Primer (qPCR): mouse Arg1 Forward: 5’-GTGAAGAACCCACGGTCTGT-3’ | This paper | N/A |
| Primer (qPCR): mouse Arg1 Reverse: 5’-CTGGTTGTCAGGGGAGTGTT-3’ | This paper | N/A |
| Primer (qPCR): mouse Gapdh Forward: 5’-GGTGCTGAGTATGTCGTGGA-3’ | This paper | N/A |
| Primer (qPCR): mouse Gapdh Reverse: 5’-CGGAGATGATGACCCTTTTG-3’ | This paper | N/A |
| Primer (qPCR): mouse Il1b Forward: 5’-CCCAAGCAATACCCAAAGAA-3’ | This paper | N/A |
| Primer (qPCR): mouse Il1b Reverse: 5’-GCTTGTGCTCTGCTTGTGAG-3’ | This paper | N/A |
| Primer (qPCR): mouse Il6 Forward: 5’-TGTTCTCTGGGAAATCGTGGA-3’ | This paper | N/A |
| Primer (qPCR): mouse Il6 Reverse: 5’-AAGTGCATCATCGTTGTTCATACA-3’ |
This paper | N/A |
| Primer (qPCR): mouse Il12b Forward: 5’-AGGTCACACTGGACCAAAGG-3’ | This paper | N/A |
| Primer (qPCR): mouse Il12b Reverse: 5’-TGGTTTGATGATGTCCCTGA-3’ | This paper | N/A |
| Primer (qPCR): mouse Nos2 Forward: 5’-CACCTTGGAGTTCACCCAGT-3’ | This paper | N/A |
| Primer (qPCR): mouse Nos2 Reverse: 5’-ACCACTCGTACTTGGGATGC-3’ | This paper | N/A |
| Primer (qPCR): mouse Nr4a1 Forward: 5’-TTGAGTTCGGCAAGCCTACC-3’ | This paper | N/A |
| Primer (qPCR): mouse Nr4a1 Reverse: 5’-GTGTACCCGTCCATGAAGGTG-3’ | This paper | N/A |
| Primer (qPCR): mouse Ptgs2 Forward: 5’-GCGAGCTAAGAGCTTCAGGA-3’ | This paper | N/A |
| Primer (qPCR): mouse Ptgs2 Reverse: 5’-TCATACATTCCCCACGGTTT-3’ | This paper | N/A |
| Primer (qPCR): mouse Retnla Forward: 5’-TGCTGGGATGACTGCTACTG-3’ | This paper | N/A |
| Primer (qPCR): mouse Retnla Reverse: 5’-CTGGGTTCTCCACCTCTTCA-3’ | This paper | N/A |
| Primer (qPCR): mouse Tnf Forward: 5’-GCACAGAAAGCATGATCCG-3’ | This paper | N/A |
| Primer (qPCR): mouse Tnf, Reverse: 5’-GCCCCCCATCTTTTGGG-3’ | This paper | N/A |
| Primer (qPCR): mouse Vegf Forward: 5’-CGAGCTCATGGACGGGTGAG-3’ | This paper | N/A |
| Primer (qPCR): mouse Vegf Reverse: 5’-GCCTGGGACCACTTGGCAT-3’ | This paper | N/A |
| ChIP-qPCR primers (see Table S1) | This paper | N/A |
| NR4A1 (Nur77) siRNA | Santa Cruz Biotechnology | Sc36110 |
| Control siRNA | Santa Cruz Biotechnology | sc-37007 |
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| Software and algorithms | ||
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| GraphPad Prism 9 | GraphPad Software Inc. | RRID: SCR_002798 |
| FlowJo 10 | Becton Dickinson & Company | RRID: SCR_008520 |
| ImageJ | NIH | RRID: SCR_003070 |