REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
primary mouse anti-human CD14 (Clone MφP9)	BD Biosciences	cat. no. 347490; RRID:AB_400310
AlexaFluor 488 secondary goat anti-mouse antibody	Biolegend	cat. no. 405319; RRID: AB_2563044
Biological Samples
Human colon organoids HC176	Harvard digestive disease center	N/A
Human colon organoids HC100	Yilmaz lab at the Koch Institute/MIT	N/A
Human Peripheral blood Leuko Pak	StemCell	cat. no. 70500
Human primary hepatocytes	BioIVT	cat. no. AQL
Human primary Kupffer cells	Thermo Fisher	cat. no. HUKCCS
Chemicals, Peptides, and Recombinant Proteins
L-WRN conditioned medium	ATCC	cat. no. CRL-3276
Murine EGF	Thermo Fisher	cat. no. PMG8041
N2 supplement	Thermo Fisher	cat. no. 17502–048
B-27 Supplement	Thermo Fisher	cat. no. 17502–044
Human [Leu15]-gastrin I	Sigma	cat. no. G9145
Thiazovivin	Tocris	cat. no. 3845
SB202190	Tocris	cat. no. 1264
A83–01	Tocris	cat. no. 2939
Prostaglandin E2	StemCell	cat. no. 72192
Cell Recovery Solution	Corning	cat. no. 354253
Growth factor-reduced Matrigel	Becton Dickinson	cat. no. 356237
Recombinant human noggin	Peprotech	cat. no. 120–10C
R-spondin conditioned medium	Sigma	cat. no. SCC111
Recombinant human GM-CSF	Biolegend	cat. no. 572903
Recombinant human IL-4	Biolegend	cat. no. 574004
Recombinant Human M-CSF	Biolegend	cat. no. 716602
Recombinant Human IL-2	R&D Systems	cat. no. 202-IL
William’s E medium	Thermo Fisher	cat. no. A1217601
Plating Supplement Pack	Thermo Fisher	cat. no. CM3000
Cell Maintenance Supplement Pack	Thermo Fisher	cat. no. CM4000
ImmunoCult Human CD3/CD28 T cell activator	StemCell	cat. no. 10971
Recombinant Human TGF-beta	R&D Systems	cat. no. 240-B/CF
Recombinant Human IL-6	R&D Systems	cat. no. 206-IL
Recombinant Human IL-1	R&D Systems	cat. no. 201-LB
Recombinant Human IL-12	R&D Systems	cat. no. 212-IL
Recombinant Human IFN-γ	R&D Systems	cat. no. 285-IF
NucBlue	Invitrogen	cat. no. 12303553
Actin Red	Invitrogen	cat. no. 15119325
Prolong Diamond Antifade	Invitrogen	cat. no. 15205739
PureLink RNA mini kit	Thermo Fisher	cat. no. 12183018A
Kapa RNA HyperPrep with RiboErase	Kapa Biosystems	cat. no. 08098107702
Critical Commercial Assays
Albumin ELISA	Bethyl Laboratories	cat. no. E80–129
EasySep Human Naïve CD4+ T Cell Isolation Kit II	StemCell	cat. no. 17555
EasySep Human Monocyte Enrichment Kit	StemCell	cat. no. 19058
MILLIPLEX MAP Human Cytokine/Chemokine Magnetic Bead Panel - Premixed 41 Plex Kit	Millipore Sigma	cat. no. HCYTMA-G60K-PX41
MILLIPLEX MAP TGFß Magnetic Bead 3 Plex Kit	Millipore Sigma	cat. no. TGFBMAG-64K-03
MILLIPLEX MAP Human Th17 Panel plex Kit	Millipore Sigma	cat. no. HTH17MAG-14K-10
Deposited Data
Raw RNAseq data	This paper	GEO: GSE135428
Software and Algorithms
ZEN software	ZEISS	https://www.zeiss.com/microscopy/us/products/microscopesoftware/zenlite.html
Analyst 1.6.2.	SCIEX	https://sciex.com/software-support/softwaredownloads
xPONENT for FLEXMAP 3D software 4.2	Luminex Corporation	https://www.luminexcorp.com/
Bio-Plex Manager Software	BioRad	http://www.biorad.com/enus/product/bio-plexmanager-softwarestandardedition?ID=5846e84e-03a7-4599-a8ae7ba5dd2c7684; RRID:SCR_014330
ClustVis	BIIT Research Group	https://biit.cs.ut.ee/clustvis/; RRID:SCR_017133
Prism 8.0	GraphPad Software	https://www.graphpad.com/scientificsoftware/prism/; RRID:SCR_002798
BioVinci	BioTuring	https://vinci.bioturing.com/
ArrayStudio	QIAGEN	https://www.omicsoft.com/array-studio
Rstudio	The Rstudio team	https://www.rstudio.com/; RRID:SCR_000432
Matlab	Mathworks	https://www.mathworks.com/products/matlab.html; RRID:SCR_001622
BWA version 0.7.12		http://bio-bwa.sourceforge.net/; RRID:SCR_010910
Bedtools v. 2.25.0.	Bedtools	https://bedtools.readthedocs.io/en/latest/content/history.html; RRID:SCR_006646
STAR v. 2.5.3a	Dobin et al. 2013	https://github.com/alexdobin/STAR; RRID:SCR_015899
RSEM v. 1.3.0	Li and Dewey, 2011	https://deweylab.github.io/RSEM/; RRID:SCR_013027
DESeq2 1.12.3	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html; RRID:SCR_015687
Spotfire	Tibco	https://www.tibco.com/products/tibcospotfire; RRID:SCR_008858
GSEA v 2.2.3.	Broad Institute	http://software.broadinstitute.org/gsea/; RRID:SCR_003199
plot.ly	Plotly	https://plot.ly/; RRID:SCR_013991
Enrichr	the Ma’ayan Lab/Icahn School of Medicine at Mount Sinai	https://amp.pharm.mssm.edu/Enrichr/; RRID:SCR_001575
ClueGO	Bindea et al., 2009	https://omictools.com/cluego-tool; RRID:SCR_005748
Cytoscape v3.7.1	Cytoscape Consortium	http://www.cytoscape.org; RRID:SCR_003032
MetaboAnalyst 4	Xia Lab at McGill Univeristy	https://www.metaboanalyst.ca; RRID:SCR_015539
Venny 2.0.	Oliveros, 2007–2015	https://bioinfogp.cnb.csic.es/tools/venny/; RRID:SCR_016561