Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Bacteroides thetaiotaomicron) | VPI-5482 Δtdk ΔCPS | Rogers et al., 2013 | Referred to as ‘B. theta’ in the text | Acapsular mutant provided by Eric Martens’s lab |
| Strain, strain background (Bacteroides thetaiotaomicron) | VPI-5482 Δtdk ΔBT1854 ΔBT2152 | Jacobson et al., 2018 | Referred to as ‘B. theta 4PP’ in the text | Mutant producing tetra-acylated, di-phosphorylated lipid A in a capsule-producing background |
| Biological sample (human) | PBMCs | AllCells | Freshly isolated from de-identified healthy individuals and shipped overnight | |
| Antibody | Anti-human CD14 (clone HCD14, mouse monoclonal), PE, PerCP-Cy5.5, or BV421 | BioLegend | PE: Cat#: 325605; RRID:AB_830678
PerCP-Cy5.5: Cat#:325621; RRID:AB_893252 BV421: 325627; RRID:AB_2561342 |
Flow cytometry (2 µL per test) |
| Antibody | Anti-human CD80 (clone 2D10, mouse monoclonal), APC | BioLegend | Cat#: 305219; RRID:AB_2291403 | Flow cytometry (5 µL per test) |
| Antibody | Anti-human CD83 (clone HB15e, mouse monoclonal), APC-Cy7 | BioLegend | Cat#: 305329; RRID:AB_2566392 | Flow cytometry (4 µL per test) |
| Antibody | Anti-human CD86 (clone BU63, mouse monoclonal), FITC or BV605 | BioLegend | FITC: Cat#: 374203; RRID:AB_2721573
BV605: Cat#: 374213; RRID:AB_2734429 |
Flow cytometry (5 µL per test) |
| Antibody | Anti-human HLA-DR (clone L243, mouse monoclonal), PE or FITC | BioLegend | PE: Cat#: 307605; RRID:AB_314683
FITC: Cat#: 307603; RRID:AB_314681 |
Flow cytometry (5 µL per test) |
| Antibody | Anti-human CD11b (clone LM2, mouse monoclonal), PE-Cy7 | BioLegend | Cat#: 393103; RRID:AB_2734450 | Flow cytometry (5 µL per test) |
| Antibody | Anti-human CD11c (clone Bu15, mouse monoclonal), Pacific Blue, FITC, or PerCP-Cy5.5 | BioLegend | Pacific Blue: Cat#: 337212; RRID:AB_1595430
FITC: Cat#: 337213; RRID:AB_1877174 PerCP-Cy5.5: Cat#: 337209; RRID:AB_1279071 |
Flow cytometry (5 µL per test) |
| Antibody | Anti-human CD205 (clone HD30, mouse monoclonal), PE | BioLegend | Cat#: 342203; RRID:AB_1626209 | Flow cytometry (5 µL per test) |
| Antibody | Anti-human B2M (clone 2M2, mouse monoclonal), PE | BioLegend | Cat#: 316306; RRID:AB_492839 | Flow cytometry (2 µL per test) |
| Antibody | Anti-human TLR4 (clone HTA125, mouse monoclonal), APC | BioLegend | Cat#: 312815; RRID:AB_2562486 | Flow cytometry (4 µL per test) |
| Sequence-based reagent | Purified sgRNAs | This paper/Synthego | Library available from Synthego as ‘Pattern Recognition Receptors and Signaling Pathway arrayed library’ | Sequences and genomic binding locations listed in Supplementary file 1 |
| Sequence-based reagent | Genomic locus amplification primers | This paper | Sequences listed in Supplementary file 1 | |
| Sequence-based reagent | qPCR primers against ACTB, IFNB1, TNF, CXCL10 | Universal Probe Library (Roche) | Sequences included in Materials and methods section | |
| Peptide, recombinant protein | Human GM-CSF | Gemini Bio | Cat#: 300–124P | Used at 50 ng/mL in DC differentiation medium |
| Peptide, recombinant protein | Human IL-4 | Gemini Bio | Cat#: 300–154P | Used at 20 ng/mL in DC differentiation medium |
| Peptide, recombinant protein | Streptococcus pyogenes Cas9 2xNLS | Synthego | Available via Synthego as an ‘Add-On Product’ | |
| Commercial assay or kit | EasySep human monocyte enrichment kit (with or without CD16 depletion) | Stemcell Technologies | With CD16 depletion: Cat# 19059 Without CD16 depletion: Cat# 19058 |
|
| Commercial assay or kit | SimpleStep human TNF alpha ELISA kit | Abcam | Cat#: ab181421 | |
| Commercial assay or kit | SimpleStep human IP-10 ELISA kit |
Abcam | Cat#: ab173194 | |
| Commercial assay or kit | SimpleStep human IL-10 ELISA kit | Abcam | Cat#: ab185986 | |
| Commercial assay or kit | Stranded mRNA prep ligation kit | Illumina | Cat#: 20040534/20040532 | |
| Chemical compound, drug | Ultrapure E. coli O55:B5 LPS | Invivogen | Cat#: TLRL-PB5LPS | |
| Chemical compound, drug | Rhodobacter sphaeroides LPS | Invivogen | Cat#: TLRL-RSLPS | |
| Chemical compound, drug | Bacteroides thetaiotaomicron WT LPS (ΔCPS) | Jacobson et al., 2018 this paper | Referred to as ‘B. theta LPS’ or ‘B. theta WT LPS (ΔCPS)’ in the text | |
| Chemical compound, drug | Bacteroides thetaiotaomicron 4PP LPS | Jacobson et al., 2018 this paper | Referred to as ‘B. theta 4PP LPS’ in the text | |
| Software, algorithm | Knock-knock v0.3 | https://github.com/jeffhussmann/knock-knock and Canaj et al., 2019 | ||
| Other | Ghost Dye Violet 510 | Tonbio Biosciences | Cat#: 13–0870 T100 | Flow cytometry viability stain (0.1 µL per 100 µL cells) |