| Antibodies |
|
|
|
| ATF3 |
CST |
D2Y5W; RRID: AB_2799039 |
| ATF4 |
CST |
D4B8; RRID: AB_2616025 |
| JUN |
CST |
60A8; RRID: AB_2130165 |
| JUNB |
Abcam |
245500; RRID: AB_2904574 |
| pJUNSer63
|
CST |
2361; RRID: AB_490908 |
| FOSL1 |
Santa Cruz |
376148; RRID: AB_11012022 |
| FOSL2 |
Santa Cruz |
sc-166102, RRID:AB_2107079 |
| IRF1 |
Abcam |
ab191032; RRID: AB_2904575 |
| IRF7 |
Abcam |
ab115352, RRID:AB_10862356 |
| PFKFB3 |
Proteintech |
13763-1-AP, RRID:AB_2162854 |
| SLC2A1 |
Abcam |
ab115730, RRID:AB_10903230 |
| SOAT2 |
Santa Cruz |
sc-59443, RRID:AB_10611790 |
| Donkey anti-mouse 488 |
ThermoFisher |
A-21202, RRID:AB_141607 |
| Donkey anti-rabbit 555 |
ThermoFisher |
A-31572, RRID:AB_162543 |
| LDH |
Santa Cruz |
sc-33781, RRID:AB_2134947 |
| ENO2 |
Proteintech |
10149-1-AP, RRID:AB_2099180 |
| iNOS |
Abcam |
ab53004, RRID:AB_869050 |
| SLC2A1 |
Santa Cruz |
sc-7903, RRID:AB_2190936 |
| TUBULIN |
CST |
3873, RRID:AB_1904178 |
| HPR-conjugated anti-mouse IgG |
CST |
7076, RRID:AB_330924 |
| HPR-conjugated anti-rabbit IgG |
CST |
7074, RRID:AB_2099233 |
|
| Chemicals, peptides, and recombinant proteins |
|
|
|
| KAPA SYBR FAST qPCR Master mix (2X) |
Kapa Biosystems |
Cat#07959427001 |
| Dynabeads Protein A |
Thermo Fisher Scientific |
Cat#10002D |
| Dynabeads Protein G |
Thermo Fisher Scientific |
Cat#10004D |
| SpeedBeads magnetic carboxylate modified particles |
GE Healthcare |
Cat#65152105050250 |
| TRIzol Reagent |
Thermo Fisher Scientific |
Cat#15596018 |
| Formaldehyde |
Thermo Fisher Scientific |
Cat#BP531-500 |
| Disuccinimidyl glutarate |
ProteoChem |
Cat#c1104-100mg |
| Oligo d(T)25 Magnetic Beads |
NEB |
Cat#S1419S |
| DTT |
Thermo Fisher Scientific |
Cat#P2325 |
| SUPERase-In |
Ambion |
Cat#AM2696 |
| Oligo dT primer |
Thermo Fisher Scientific |
Cat#18418020 |
| Agencourt RNA Clean XP Beads |
Beckman Coulter |
Cat#A63987 |
| 10 X Blue Buffer |
Enzymatics |
Cat#P7050L |
| DNA polymerase I |
Enzymatics |
Cat#P7050L |
| Random primers |
Thermo Fisher Scientific |
Cat#48190011 |
| SuperScript III Reverse Transcriptase |
Thermo Fisher Scientific |
Cat#18080044 |
| 5 X first-strand buffer |
Thermo Fisher Scientific |
Cat#18080044 |
| Actinomycin D |
Sigma |
Cat#A1410 |
| DNaseI |
Worthington |
Cat#LS002139
|
| SP600A125 |
Tocris |
#1496 |
| BAY-876 |
Selleckchem |
#S8452 |
| MAPK P38 inhibitor SB203580 |
Tocris |
#1202 |
| NLRP3 inflammasome inhibitor MCC950 |
Selleckchem |
#S7809 |
| BHA |
Sigma |
#B1253 |
| Lipofectamine™ RNAiMAX Transfection Reagent |
Invitrogen |
#13778150 |
| Ficoll Plaque Premium |
Sigma GE Healthcare |
#17-544-02 |
| Recombinant human M-CSF |
Stem Cell |
#78057-2 |
| BD Cytofix/Cytoperm Buffer |
BD |
#BD554714 |
| BD Wash and Permeabilization Buffer |
BD |
#BD554714 |
| Phalloidin |
Sigma |
#176759 |
| Prolong Gold Antifade Reagent |
Life Technologies |
#10144 |
|
| Critical commercial assays |
|
|
|
| Direct-zol RNA MicroPrep Kit |
Zymo Research |
Cat#R2062 |
| Qubit dsDNA HS Assay Kit |
Invitrogen |
Cat#Q32851
|
| Superscript III First-Strand Synthesis System |
Thermo Fisher Scientific |
Cat#18080051 |
| BD Vacutainer CPT Tubes |
BD Biosciences |
#362753 |
| BCA Assay |
BioRad |
#500–0006 |
| Western Lighting Plus ECL reagent |
Perkin |
#0RT2655/0RT2755 |
|
| Deposited data |
|
|
|
| Raw and Analyzed data |
GEO |
GSE191054 |
|
| Experimental models: Cell lines |
|
|
|
| C57BL/6 J mice |
The Jackson Laboratory |
RRID: IMSR_JAX:000664 |
| L929 |
ATCC |
CRL-6364 |
|
| Experimental models: Organisms/strains |
|
|
|
| MyD88−/− mice |
The Jackson Laboratory |
009088 |
|
| Oligonucleotides |
|
|
|
| siControl |
Dharmaphect |
D-001210-02 |
| siJun |
Dharmaphect |
#L-043776-00–0005 |
| siFosl1 |
Dharmaphect |
#L-040704-00–0005 |
| Primers for qPCR and ChIP-qPCR |
|
Table S6
|
|
| Software and algorithms |
|
|
|
| Bowtie2 (Langmead and Salzberg, 2012) |
|
http://bowtie-bio.sourceforge.net/bowtie2/
|
| HOMER (Heinz et al., 2010) |
|
http://homer.ucsd.edu/homer/
|
| R package: DeSeq2 (Love et al., 2014) |
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| STAR (Dobin et al., 2013) |
|
https://github.com/alexdobin/STAR
|
| UCSC Genome Browser (Kent et al., 2002) |
|
https://genome.ucsc.edu/
|
| RStudio |
RStudio |
https://www.rstudio.com/
|
| Pathway Analysis (Liberzon et al., 2011, 2015; Subramanian et al., 2005) |
GSEA |
http://www.gsea-msigdb.org/gsea/login.jsp
|
