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. Author manuscript; available in PMC: 2020 May 21.
Published in final edited form as: Immunity. 2019 May 7;50(5):1172–1187.e7. doi: 10.1016/j.immuni.2019.04.004

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