KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-mouse CD3 | BD, Biolegend | Clone 17A2 |
| anti-mouse CD4 | Biolegend | Clone GK1.5 |
| anti-mouse CD4 | BD | Clone RM4-5 |
| anti-mouse CD8 | BD, Biolegend | Clone 53-6.7 |
| anti-mouse CD16/32 (Fc Block) | BD | Clone 2.4G2 |
| anti-mouse CD19 | Biolegend | Clone 6D5 |
| anti-mouse CD28 | BD | Clone 37.51 |
| anti-mouse CD38 | eBioscience | Clone 90 |
| anti-mouse B220 | BD, eBioscience | Clone RA3-6B2 |
| anti-mouse CD45.1 | BD, eBioscience | Clone A20 |
| anti-mouse CD45.2 | BD, eBioscience | Clone 104 |
| anti-mouse CD93 | Biolegend, eBioscience | Clone AA4.1 |
| anti-mouse CD138 | BD, Biolegend | Clone 281-2 |
| anti-mouse CXCR3 | eBioscience | Clone CXCR3-173 |
| anti-mouse IL-4 | BioXCell | Clone 11B11 |
| anti-mouse IFNγ | BioXCell | Clone XMG1.2 |
| anti-mouse IgM F(ab’)2 | Southern Biotech | Polyclonal, goat |
| anti-mouse IgM | eBioscience | Clone II-41 |
| anti-mouse IgD | BD | Clone AMS 9.1 |
| anti-mouse IgD | Biolegend | Clone 11-26c.2a |
| anti-mouse heavy chain-specific IgG1 | Biolegend | Clone RMG1-1 |
| anti-mouse heavy chain-specific IgG2b | Biolegend | Clone RMG2b-1 |
| anti-mouse heavy chain-specific IgG2b | Southern Biotech | Polyclonal, goat |
| anti-mouse heavy chain-specific IgG2c | Southern Biotech | Polyclonal, goat |
| anti-mouse kappa light chain | Southern Biotech | Polyclonal, goat |
| anti-mouse Ig, heavy and light chain | Southern Biotech | Polyclonal, goat |
| anti-mouse T-bet | eBioscience | Clone 4B10 |
| anti-mouse heavy chain-specific pan-IgG | Jackson ImmunoResearch | Cat#315-056-046 |
| Bacterial and Virus Strains | ||
| H1N1 influenza virus, A/PR/8/34 (PR8) | (Allie et al., 2019) | |
| H3N2 influenza virus, A/Aichi/68 (X31) | (Allie et al., 2019) | |
| Heligmosomoides polygyrus (Hp) | (Leon et al., 2012) | |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Pin-X, pyrantel pamoate | Quartz Pharmaceuticals | NDC 13893-691-49 |
| Tamoxifen | Sigma | Cat#T5648 |
| Mitomycin C | Sigma | Cat#M4287 |
| OVA(323-339) peptide (OT-II) | New England Peptide | Cat# BP10-910 |
| Betulinic acid | Abcam | Cat#AB120654 |
| R848 | InvivoGen | Cat#tlrl-r848 |
| CpG ODN1826 | InvivoGen | Cat#tlrl-1826 |
| recombinant IL-2 | PreproTech | Cat#212-12 |
| recombinant IL-4 | PreproTech | Cat#214-14 |
| recombinant IL-12 | Genetics Institute | |
| PNA (lectin) Pacific Blue conjugate | Sigma | L0881 |
| recombinant flu nucleoprotein tetramer | (Allie et al., 2019) | |
| purified PR8 virus proteins | (Lee et al., 2005) | |
| Heligmosomoides polygyrus (Hp) extract | (Harris et al., 2000) | |
| 7-aminoactinomycin D (7AAD) | Sigma | Cat#A9400-1MG |
| LIVE/DEAD Fixable Dead Cell Stains | ThermoFisher | Cat#L34960 |
| Neutral Buffered Formalin Solution, 10% | Sigma | Cat#HT501128 |
| Alkaline phosphatase substrate BCIP/NBT | Moss Substrates | Cat#NBIM-1000 |
| Lymphocyte separation media | Corning | Cat#B003L38 |
| TRIzol Reagent | ThermoFisher | Cat#15596026 |
| TaqMan Gene Expression Master Mix | Applied Biosystems | Cat#4369016 |
| TaqMan Gene Expression Assay Batf | Applied Biosystems | Mm00479410_m1 |
| TaqMan Gene Expression Assay Bcl6 | Applied Biosystems | Mm00477633_m1 |
| TaqMan Gene Expression Assay Cxcl10 | Applied Biosystems | Mm00445235_m1 |
| TaqMan Gene Expression Assay Ets1 | Applied Biosystems | Mm01175819_m1 |
| TaqMan Gene Expression Assay Gapdh | Applied Biosystems | Mm99999915_g1 |
| TaqMan Gene Expression Assay Hif1a | Applied Biosystems | Mm00468869_m1 |
| TaqMan Gene Expression Assay Ifih1 | Applied Biosystems | Mm00459183_m1 |
| TaqMan Gene Expression Assay Ifng | Applied Biosystems | Mm01168134_m1 |
| TaqMan Gene Expression Assay Ifngr2 | Applied Biosystems | Mm01210592_m1 |
| TaqMan Gene Expression Assay Il6 | Applied Biosystems | Mm00446190_m1 |
| TaqMan Gene Expression Assay Irf4 | Applied Biosystems | Mm00516431_m1 |
| TaqMan Gene Expression Assay Irf5 | Applied Biosystems | Mm00496447_m1 |
| TaqMan Gene Expression Assay Irf7 | Applied Biosystems | Mm00516788_m1 |
| TaqMan Gene Expression Assay Jun | Applied Biosystems | Mm00495062_s1 |
| TaqMan Gene Expression Assay Pax5 | Applied Biosystems | Mm00435501_m1 |
| TaqMan Gene Expression Assay Pou2af1 | Applied Biosystems | Mm004488326_m1 |
| TaqMan Gene Expression Assay Prdm1 | Applied Biosystems | Mm00476128_m1 |
| TaqMan Gene Expression Assay Relb | Applied Biosystems | Mm00485664_m1 |
| TaqMan Gene Expression Assay Rorc | Applied Biosystems | Mm01261022_m1 |
| TaqMan Gene Expression Assay Runx3 | Applied Biosystems | Mm00490666_m1 |
| TaqMan Gene Expression Assay Spib | Applied Biosystems | Mm03048233_m1 |
| TaqMan Gene Expression Assay Stat2 | Applied Biosystems | Mm00490880_m1 |
| TaqMan Gene Expression Assay Stat4 | Applied Biosystems | Mm00448881_m1 |
| TaqMan Gene Expression Assay Tbkbp1 | Applied Biosystems | Mm00446590_m1 |
| TaqMan Gene Expression Assay Tbx21 | Applied Biosystems | Mm00450960_m1 |
| TaqMan Gene Expression Assay Tlr7 | Applied Biosystems | Mm00446590_m1 |
| TaqMan Gene Expression Assay Tnfsf4 | Applied Biosystems | Mm00437214_m1 |
| TaqMan Gene Expression Assay Tnfsf10 | Applied Biosystems | Mm01283606_m1 |
| TaqMan Gene Expression Assay Xbp1 | Applied Biosystems | Mm00457359_m1 |
| Critical Commercial Assays | ||
| eBioscience Foxp3 / Transcription Factor Staining Buffer Set | ThermoFisher | Cat#00-5523-00 |
| RNeasy Micro Kit | Qiagen | Cat#74004 |
| Invitrogen SuperScript II Reverse Transcriptase | ThermoFisher | Cat#18064 |
| Next High-Fidelity Taq 2× Master Mix | New England BioLabs | Cat#M0270L |
| Nextera DNA Library Preparation Kit | Illumina | Cat#FC-121-1030 |
| TruSeq RNA Library Prep Kit | Illumina | Cat#RS-122-2001 |
| PCR Purification Kit | Qiagen | Cat#28104 |
| MinElut Kit | Qiagen | Cat#28004 |
| Affymetrix GeneChip Mouse Genome U430 Plus 2.0 Array | ThermoFisher | Cat#900497 |
| Affymetrix one-cycle cDNA synthesis kit | ThermoFisher | Cat#10752030 |
| Affymetrix IVT Labeling Kit | ThermoFisher | Cat#900449 |
| Deposited Data | ||
| Microarray data | this paper | GEO: GSE84948 |
| RNA-seq data | this paper | GEO: GSE83697 |
| ATAC-seq data | this paper | GEO: GSE118984 |
| Experimental Models: Organisms/Strains | ||
| C57BL/6-Tg(TcraTcrb)425Cbn/J (OT-II) | Jackson Laboratory | |
| B6.SJL-Ptprca Pepcb/BoyJ (CD45.1+) | Jackson Laboratory | |
| B6.129S7-Ifngr1tm1Agt/J (Ifngr1−/−) | Jackson Laboratory | |
| B6.129P2(C)-Cd19tm1(Cre)Cgn/J (Cd19Cre/+) | Jackson Laboratory | |
| B6.129-Tbx2tm2Srnr/J (Tbx21Cl/fl) | Jackson Laboratory | |
| B6.129-Prdm1tm1Clme/J (Prdm1fl/fl) | Jackson Laboratory | |
| B6.129S2-Ighmtm1Cgn/J (μMT) | Jackson Laboratory | |
| hCD20-TAM-cre | Mark Shlomchik (Khalil et al., 2012) | |
| B6.Blimp1-YFP | Eric Meffre (Rutishauser et al., 2009) | |
| B6.T-bet-ZsGreen | Jinfang Zhu (Zhu et al., 2012) | |
| Software and Algorithms | ||
| Bowtie | (Langmead et al., 2009) | http://bowtie-bio.sourceforge.net/index.shtml |
| FASTX-Toolkit | http://hannonlab.cshl.edu/fastx_toolkit/ | |
| FlowJo | Tree Star | https://www.flowjo.com/ |
| R/Bioconductor & edgeR | (Robinson et al., 2010) | https://www.bioconductor.org/ |
| Genomic Ranges R/Bioconductor package | (Lawrence et al., 2013) | |
| GraphPad Prism | GraphPad Software | |
| GSEA program | (Subramanian et al., 2005) | http://software.broadinstitute.org/gsea/index.jsp |
| HOMER, analyzeRepeats.pl, annotatePeaks.pl, findPeaks.pl, findMotifs.pl, findMotifsGenome.pl, getDiffExpression.pl –repeats, and mergePeaks.pl scripts | (Heinz et al., 2010) | http://homer.ucsd.edu/homer/ |
| Ingenuity Pathway Analysis (IPA) | https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis/ | |
| IPA upstream regulator analysis | (Kramer et al., 2014) | |
| MATLAB | The Mathworks Inc. | https://www.mathworks.com/products/matlab.html |
| Microarray Suite 5 (MAS5) algorithm | Affymetrix | |
| PageRank analysis | (Yu et al., 2017) | |
| Picard Tools MarkDuplicates function | http://broadinstitute.github.io/picard/ | |
| TopHat2 | (Kim et al., 2013) | https://ccb.jhu.edu/software/tophat/index.shtml |