KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| PE-CF594 anti-NK-1.1 (Myeloid Panel) | BD | Cat#: 562864; RRID: AB_2737850 |
| PE-CF594 anti-γδ TCR (Myeloid Panel) | BD | Cat#: 563532; RRID: AB_2661844 |
| PE-CF594 anti-TCRβ (Myeloid Panel) | BD | Cat#: 562841; RRID: AB_2737831 |
| PE-CF594 anti-CD45R/B220 (Myeloid Panel) | BD | Cat#: 562313; RRID: AB_11151901 |
| FITC anti-Ly6C (Myeloid Panel) | BD | Cat#: 553104; RRID: AB_394628 |
| AF700 anti-I-A/I-E (Myeloid Panel) | BioLegend | Cat#: 107621; RRID: AB_493726 |
| APC/Cy7 anti-CD11b (Myeloid Panel) | BioLegend | Cat#: 101226; RRID: AB_830642 |
| PE anti-CCR2 (Myeloid Panel) | R&D | Cat#: FAB5538P; RRID: AB_10718414 |
| BV510 anti-CD24 (Myeloid Panel) | BioLegend | Cat#: 101831; RRID: AB_2563894 |
| PerCP/Cy5.5 anti-CD64 (Myeloid Panel) | BioLegend | Cat#: 139307; RRID: AB_2561963 |
| APC anti-CD11c (Myeloid Panel) | BioLegend | Cat#: 117309; RRID: AB_313778 |
| BV785 anti-CX3CR1 (Myeloid Panel) | BioLegend | Cat#: 149029; RRID: AB_2565938 |
| BV650 anti-Ly6G (Myeloid Panel) | BioLegend | Cat#: 127641; RRID: AB_2565881 |
| BV605 anti-CD103 (Myeloid Panel) | BioLegend | Cat#: 121433; RRID: AB_2629724 |
| Pacific Blue anti-CD45 (Myeloid/Adaptive Panels) | BioLegend | Cat#: 103126; RRID: AB_493535 |
| FITC anti-CD62L (Adaptive Panel) | BioLegend | Cat#: 104405; RRID: AB_313092 |
| APC/Cy7 anti-NK-1.1 (Adaptive Panel) | BioLegend | Cat#: 108723; RRID: AB_830870 |
| PE/Cy7 anti-CD44 (Adaptive Panel) | BioLegend | Cat#: 103029; RRID: AB_830786 |
| APC anti-CD45R/B220 (Adaptive Panel) | BioLegend | Cat#: 100206; RRID: AB_312663 |
| BV605 anti-CD4 (Adaptive Panel) | BioLegend | Cat#: 100451; RRID: AB_2564591 |
| BV711 anti-CD8α (Adaptive Panel) | BioLegend | Cat#: 100747; RRID: AB_11219594 |
| TruStain FcX | BioLegend | Cat#: 101319; RRID: AB_1574973 |
| Zombie UV Fixable Viability Kit | BioLegend | Cat#: 423107 |
| Fixation Buffer | eBioscience | Cat#: 00-5523-00 |
| Anti-Histone H3 | abcam | Cat#: ab1791; RRID: AB_302613 |
| Anti-S100A8 | abcam | Cat#: ab92331; RRID: AB_2050283 |
| Biological samples | ||
| Crohn’s disease peripheral blood mononuclear cells | PRISM Cohort, MGH | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| RPMI media | Life technologies | Cat#: 11875-093 |
| DMEM media | Life technologies | Cat#: 11995-073 |
| Dextran Sulfate Sodium (DSS) | MP Biomedicals | Cat#: 160110; CAS: 9011-18-1 |
| Hyclone fetal bovine serum | GE Healthcare | S#30396.03 |
| Penicillin-Streptomycin | Gibco | P4333 |
| Ficoll-Paque Plus | GE Healthcare | 17-1440-02 |
| RNAiMAX | Life Technologies | 13778075 |
| HiPerfect Transfection Reagent | Qiagen | 1029975 |
| LPS 0111:B4 | Sigma | L4391 |
| Metronidazole | RPI | Cat#: M81000; CAS: 443-48-1 |
| Ampicilin | RPI | Cat#: 69-52-3; CAS: 69-52-3 |
| Neomycin | Sigma Aldrich | Cat#: N6386; CAS: 1405-10-3 |
| Vancomycin | Chem Impex | Cat#: 00315; CAS: 1404-93-9 |
| Dispase II | Sigma | Cat#: D4693; CAS: 42613-33-2 |
| Collagenase, Type IV | Sigma | Cat#: 17104019 |
| Recombinant murine M-CSF | Peprotech | 315-02 |
| Recombinant murine IL-3 | Peprotech | 213-13 |
| Critical commercial assays | ||
| PureLink Microbiome DNA Purification Kit | Invitrogen | A29790 |
| RNeasy mini kit | Qiagen | 74104 |
| Mouse IL-6 ELISA kit | R&D | DY406 |
| Deposited data | ||
| SP140 16S rRNA sequencing data | This paper | SRA: PRJNA818684 |
| SP140 PBMC RNA sequencing data | Mehta et al., 2017 | GEO: GSE89876 |
| Experimental models: Cell lines | ||
| Human: THP1 | Laboratory of Hans-Christian Reinecker | N/A |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL6/J | The Jackson Laboratory | JAX: 000664 |
| Mouse: SP140 Knockout (on C57BL6/J background) | Laboratory of Russell Vance | Ji et al. 2021 |
| Oligonucleotides | ||
| ON-TARGETplus Non-targeting Control Pool UGGUUUACAUGUCGACUAA, UGGUUUACAUGUUGUGUGA, UGGUUUACAUGUUUUCUGA, UGGUUUACAUGUUUUCCUA | Dharmacon/Horizon s Discovery | D-001810-10-05 |
| ON-TARGETplus Human SP140 siRNA – SMARTpool CCGAGCAGAUGUAUGAACA, CAAGAGUGAUGUAUUGUGU, GAACGUAGAGGGUCAGAAC, GGAUUAACCUGAUGGCCUA | Dharmacon/Horizon s Discovery | L-016508-00-0005 |
| Primer for Stool qPCR Total 16S F-GTGCCAGCMGCCGCGGTAA R-GACTACCAGGGTATCTAAT | IDT, this paper | N/A |
| Primer for Stool qPCR A. muciniphila F-CAGCACGTGAAGGTGGGGAC R-CCTTGCGGTTGGCTTCAGAT | IDT, this paper | N/A |
| Primer for Stool qPCR Helicobacter spp. F-GCTATGACGGGTATCC R-GATTTTACCCCTACACCA | IDT, this paper | N/A |
| Primer for Stool qPCR Enterobacteriaceae F-CATTGACGTTACCCGCAGAAGAAGC R-CTCTACGAGACTCAAGCTTGC | IDT, this paper | N/A |
| Primer for Mouse qPCR Lcn2 F-TCCTCAGGTACAGAGCTACAA R-GCTCCTTGGTTCTTCCATACA | IDT, this paper | N/A |
| Primer for Mouse qPCR Lyz2 F-ATGGAATGGCTGGCTACTATG | IDT, this paper | N/A |
| R-GGTCTCCACGGTTGTAGTTT | ||
| Primer for Mouse qPCR S100a8 F-CTTTGTCAGCTCCGTCTTCA R-TGTAGAGGGCATGGTGATTTC | IDT, this paper | N/A |
| Primer for Mouse qPCR Tbp F-TGATCAAACCCAGAATTGTTCT R-TGGTCTTCCTGAATCCCTTTA | IDT, this paper | N/A |
| Software and algorithms | ||
| QIIME 2 | Bolyen et al., 2019 | https://qiime2.org/ |
| DADA2 | Callahan et al., 2016 | N/A |
| MAFFT | Katoh et al., 2002 | N/A |
| UniFrac | Lozupone et al., 2005 | N/A |
| q2-feature-classifier | Bokulich et al., 2018 | N/A |
| LEfSe | Segata et al., 2011 | http://huttenhower.sph.harvard.edu/galaxy |
| ImageJ | Schneider et al., 2012 | https://imagej.nih.gov/ij/ |
| FlowJo software | BD | http://flowjo.com |
| Graphpad Prism v9.1.2 | Graphpad software | https://www.graphpad.com/ |
| Other | ||
| iTaq Universal SYBR Green supermix | Bio Rad | 1725124 |
| iScript cDNA Synthesis Kit | Bio Rad | 1708841 |
| Beadbug prefilled homogenizer tubes | Sigma-Aldrich | Z763799 |