KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
| ||
| Antibodies | ||
| Rabbit anti-MRC1 | Sigma Aldrich | HPA004114, RRID: AB_1846270 |
| Rabbit anti-CD68 antibody | Santa Cruz Biotechnology | SC-9139, RRID:AB_2275738 |
| Rabbit anti-F4/80 | Santa Cruz Biotechnology | SC-25830, RRID:AB_2246477 |
| Goat anti-Arg-1 | Santa Cruz Biotechnology | SC-18354, RRID:AB_2227469 |
| Rabbit anti-TGM2 | Cell Signaling Technologies | #3557, RRID:AB_2202883 |
| Rabbit anti-phospho-Stat1 (Y701) | Cell Signaling Technologies | #9167, RRID:AB_561284 |
| Rabbit anti-phospho-ERK1, Thr202/Tyr204 | Cell Signaling Technologies | #9101, RRID:AB_331646 |
| Rabbit anti-ERK1/2 | Cell Signaling Technologies | #4695, RRID:AB_390779 |
| Rabbit anti-β-actin | Lab Vision | Rb-9421-P1, RRID:AB_720056 |
| Mouse anti-β-actin | Sigma Aldrich | A5316, RRID:AB_476743 |
| Rabbit anti-PPARγ | Cell Signaling Technologies | # 2443, RRID:AB_823598 |
| Rabbit anti-phospho-STAT6 (Y641) | Cell Signaling Technologies | # 56554, RRID:AB_2799514 |
| Rabbit anti-β-tubulin | Cell Signaling Technologies | #2128, RRID:AB_823664 |
| Mouse anti-ALDH1A2 | Santa Cruz Biotechnology | sc-393204 |
| Rabbit IgG HRP Linked Whole Ab antibody | GE Healthcare | GENA934, RRID:AB_2722659 |
| Sheep Anti-Mouse IgG - Horseradish Peroxidase antibody | GE Healthcare | NA931, RRID:AB_772210 |
| Rabbit anti-H3K27ac | Abcam | ab4729, RRID:AB_2118291 |
| Rat anti-CD31 | BD Biosciences | # 550274, RRID:AB_393571 |
| Mouse anti-SMA-Cy3 conjugate (clone 1A4) | Sigma Aldrich | C6198, RRID:AB_476856 |
| Rat anti-F4/80 (conjugated with Alexa647) | BioLegend | # 123121, RRID:AB_893492 |
|
Chemicals, peptides, and recombinant proteins | ||
| PMA | Sigma Aldrich | P8139 |
| Murine M-CSF | Peprotech | #315–02 |
| Murine IL-4 | Peprotech | #214–14 |
| LPS | Sigma Aldrich | L4391 |
| Human M-CSF | Invitrogen | 14–8789-80 |
| Human IL-4 | Peprotech | #200–04 |
| Human IFNγ | Peprotech | #300–02 |
| MNase | New England Biolabs | M0247S |
| small molecule chemicals | Selleckchem or Cayman Chemicals | N/A |
|
Critical commercial assays | ||
| CellTiter-Glo luminescent cell viability assay (CTG) | Promega | G7573 |
| Steady-Glo Luciferase Assay System | Promega | E2520 |
| mRNeasy Mini Kit | QIAGEN | No. 217004 |
| TruSeq RNA Library Prep Kit V2 | Illumina | RS-122–2001 |
|
Deposited data | ||
| Proteomics | MassIVE repository | MSV000084672 |
| RNA-Seq and ChIP-Seq | GEO | GSE154347 |
|
Experimental models: cell lines and primary cells | ||
| THP-1 cell line | ATCC | Cat# TIB-202, RRID:CVCL_0006 |
| mouse BMDMs (primary cells) | JAX Labs | C57BL/6J mice |
| human PBMCs (primary cells) | iXCells Biotechnologies | 10HU-003CR100M |
| THP-1 cell line with MRC1 promoter-driven luciferase, 1.0k, clone#4 | He and Marneros, 2014 | N/A |
|
Experimental models: mice | ||
| C57BL/6J mice | JAX labs | JAX:000664 |
|
Oligonucleotides | ||
| semiquantitative RT-PCR primers | Life Technologies | N/A |
|
Software and algorithms | ||
| GelQuantNET, western blot band quantifications | Biochemlabsolutions | http://biochemlabsolutions.com/GelQuantNET.html |
| In-house developed software suite | Huttlin et al., 2010 | N/A |
| Sequest algorithm | Eng et al., 1994 | N/A |
| Ascore algorithm | Beausoleil et al., 2006 | N/A |
| GSEA | UCSD and Broad Institute | http://www.gsea-msigdb.org/gsea/login.jsp;jsessionid=CF17CD01EADE3916721F5DA4F6FEFFAA; version 4.0.2) |
| nf-core/rnaseq | Ewels et al., 2020 | https://github.com/nf-core/rnaseq |
| nf-core/chipseq | Ewels et al., 2020 | https://github.com/nf-core/chipseq |
|
Other | ||
| Chemical Libraries, 143 natural products | Selleckchem | Library L1400–01 and -02 |
| Chemical Libraries, 1836 bioactive compounds | Selleckchem | Library L1700–01 and -02 |
| Xvivo10 medium | Lonza | 04–380Q |
| Human serum AB plasma | Sigma | H4522 |