REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
H3K27Ac	Abcam	ab4729; RRID: AB_2118291
P300	Santa Cruz	sc-585; RRID: AB_2231120
PU.1	Santa Cruz	sc-352; RRID: AB_632289
JunB	Santa Cruz	sc-46x; RRID: AB_2130022
IRF8	Santa Cruz	sc-6058; RRID: AB_649510
STAT6	Santa Cruz	sc-981; RRID: AB_632450
C/EBPα	Santa Cruz	sc-61x; RRID: AB_631233
HDAC1	Abcam	ab7028; RRID: AB_305705
HDAC2	Abcam	ab7029; RRID: AB_305706
HDAC3	Abcam	ab7030; RRID: AB_305708
RNA PolII-pS5	Abcam	ab5131; RRID: AB_449369
RNA PolII-pS2	Abcam	ab5095; RRID: AB_304749
p65	Santa Cruz	sc-372; RRID: AB_632037
pro-IL-1β	R&D System	AF401-NA; RRID: AB_416684
ASC	Santa Cruz	sc22514-R; RRID: AB_2174874
NLRP3	AdipoGen	AG-20B-0014; RRID: AB_2490202
pro-caspase-1	AdipoGen	AG-20B-0042; RRID: AB_2490248
NOS2	eBioscience	12/5920; RRID: AB_2572641
Ym1	R&D Systems	BAF2446; RRID: AB_2260451
Bacterial and Virus Strains
Salmonella enterica enterica serovar Typhimurium strain SL3261	Prof. David Gray	University of Edinburgh
Chemicals, Peptides, and Recombinant Proteins
mouse recombinant IL-4	Peprotech	214-14
LPS (Salmonella enterica serotype minnesota Re 595)	Sigma Aldrich	L6261
Critical Commercial Assays
TruSeq RNA Sample Prep Kit v2 -Set A (48rxn)	Illumina	RS-122-2001
Ovation Ultralow System v2 1-16 (32rxn) without magnetic beads	Nugen	0344NB-32
TruSeq ChIP SamplePreparation Kit - Set A	Illumina	IP-202-1012
Nextera DNA Sample Preparation Kit (24 Samples)	Illumina	FC-121-1030
NEBNext Multiplex Small RNA Prep Set for Illumina (Set1)	Illumina	E7300 S
IL-1β ELISA kit	R&D System	DY401-05
FLICA 660 far-red fluorescence Caspase-1 Assay Kit	ImmunoChemistry Technologies	9122
Deposited Data
RNA-seq, ChIP-seq, GRO-seq and ATAC-seq	This paper	GEO: GSE106706
Microarray data from WT and HDAC3 KO BMDMs	(Mullican et al., 2011)	GEO: GSE33609
SMRT and NCoR ChIP-seq	(Barish et al., 2012)	GEO: GSE27060
H3K4m1 ChIP-seq	(Ostuni et al., 2013)	GEO: GSE38379
CTCF and RAD21 ChIP-seq	(Daniel et al., 2014)	SRA: SRP019970
RNA-seq data from Thio-Mac and Ne-Mac	(Thomas et al., 2012)	ArrayExpress: E-MTAB-995
Experimental Models: Cell Lines
primary bone marrow-derived macrophages	WT C57BL/6 and Stat6−/− mice	N/A
immortalized bone marrow-derived macrophages	WT C57BL/6 and Ncor1fl/flLys2 Cre mice	N/A
Experimental Models: Organisms/Strains
C57BL/6	The Jackson Laboratory	N/A
Stat6−/−	The Jackson Laboratory	N/A
Ncor1fl/fl	Prof. Johan Auwerx	N/A
Oligonucleotides
Primers for mRNA expression	This paper	see Table S6
Primers for eRNA expression	This paper	see Table S6
Primers for ChIP-qPCR experiments	This paper	see Table S6
Software and Algorithms
GraphPad Prism	GraphPad Software, Inc	https://www.graphpad.com/
Ingenuity Pathway Analysis	QIAGEN	https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/
TopHat	(Trapnell et al., 2013)	http://cole-trapnell-lab.github.io/projects/tophat/
Cufflinks	(Trapnell et al., 2013)	http://cole-trapnell-lab.github.io/projects/cufflinks/
Gene Set Enrichment Analysis (GSEA)	(Subramanian et al., 2005)	http://software.broadinstitute.org/gsea/index.jsp
DAVID 6.8	(Huang et al., 2009)	https://david.ncifcrf.gov/tools.jsp
Burrows-Wheeler Alignment Tool	(Li and Durbin, 2009)	http://bio-bwa.sourceforge.net/
MACS2	(Zhang et al., 2008)	https://github.com/taoliu/MACS
DiffBind v2.0.5	(Ross-Innes et al., 2012)	https://bioconductor.org/packages/release/bioc/html/DiffBind.html
VennMaster	(Kestler et al., 2008)	http://sysbio.uni-ulm.de/?Software:VennMaster
IGV2.3	(Thorvaldsdóttir et al., 2013)	http://software.broadinstitute.org/software/igv/igv2.3
ngs.plot	(Shen et al., 2014)	https://github.com/shenlab-sinai/ngsplot
Other
Heligmosomoides polygyrus	Prof. Richard Grencis	University of Manchester