REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
PE/Fire™ 810 anti-human CD197 (CCR7) Antibody	BioLegend	Clone: G043H7; RRID: AB_2894572; Cat#353269
BUV661 Mouse Anti-Human CD11c	BD Biosciences	Clone: B-ly6; RRID: AB_2870241; Cat#612967
BUV737 Mouse Anti-Human CD10	BD Biosciences	Clone: HI10a; RRID: AB_2869630; Cat#612826
CD14 Monoclonal Antibody (61D3), APC-eFluor™ 780	eBioscience	Clone: 61D3; RRID: AB_1834358; Cat#47-0149-42
CD16 Monoclonal Antibody (eBioCB16 (CB16)), APC-eFluor™ 780	eBioscience	Clone: eBioCB16; RRID: AB_11220086; Cat#47-0168-42
BUV615 Mouse Anti-Human CD19	BD Biosciences	Clone: HIB19; RRID: AB_2875287; Cat#751273
BUV496 Mouse Anti-Human CD19	BD Biosciences	Clone: SJ25C1; RRID: AB_2744311; Cat#564655
Brilliant Violet 605™ anti-human CD20 Antibody	BioLegend	Clone: 2H7; RRID: AB_2563398; Cat#302334
Spark NIR™ 685 anti-human CD20 Antibody	BioLegend	Clone: 2H7; RRID: AB_2860775; Cat#302366
BV480 Mouse Anti-Human CD21	BD Biosciences	Clone: B-Ly4; RRID: AB_2743893; Cat#746613
PE/Cyanine7 anti-human CD21 Antibody	BioLegend	Clone: Bu32; RRID: AB_2561576; Cat#354911
CD24 Monoclonal Antibody (SN3), PE-Alexa Fluor™ 610	Thermofisher	Clone: SN3; RRID: AB_10375871; Cat#MHCD2422
BUV395 Mouse Anti-Human CD27	BD Biosciences	Clone: L128; RRID: AB_2744349; Cat#563816
Brilliant Violet 711™ anti-human CD27 Antibody	BioLegend	Clone: O323; RRID: AB_2563809; Cat#302834
Spark Blue™ 550 anti-human CD3 Antibody	BioLegend	Clone: SK7; RRID: AB_2819984; Cat#344851
CD3 Monoclonal Antibody (UCHT1), APC-eFluor™ 780	eBioscience	Clone: UCHT1; RRID: AB_1272042; Cat#47-0038-42
BUV805 Mouse Anti-Human CD38	BD Biosciences	Clone: HB7; RRID: AB_2871359; Cat#742074
Brilliant Violet 421™ anti-human CD38 Antibody	BioLegend	Clone: HIT2; RRID: AB_10983072; Cat#303526
Mouse anti Human CD45RA	BioRad	Clone: F8-11-13; RRID: AB_871980; Cat#MCA88SBV570
BB700 Mouse Anti-Human CD71	BD Biosciences	Clone: M-A712; RRID: AB_2743458; Cat#746082
FITC anti-human CD71 Antibody	BioLegend	Clone: CY1g4; RRID: AB_1236432; Cat#334103
BV650 Mouse Anti-Human CD183	BD Biosciences	Clone: 1C6/CXCR3; RRID: AB_2740303; Cat#740603
PE/Cyanine5 anti-human CD184 (CXCR4) Antibody	BioLegend	Clone: 12G5; RRID: AB_314614; Cat#306508
BUV563 Mouse Anti-Human FCRL5 (CD307e)	BD Biosciences	Clone: 509F6; RRID: AB_2873900; Cat#749598
BUV395 Streptavidin	BD Biosciences	RRID: AB_2869553; Cat#564176
BUV737 Mouse Anti-Human IgD	BD Biosciences	Clone: IA6-2; RRID: AB_2738894; Cat#564687
APC/Fire™ 750 anti-human IgD Antibody	BioLegend	Clone: IA6-2; RRID: AB_2616988; Cat#348238
IgM Antibody (IM373) [Alexa Fluor® 532]	NOVUS	Clone: IM373; RRID: AB_2909529; Cat#NBP2-34650AF532
T-bet Monoclonal Antibody (eBio4B10 (4B10)), eFluor™ 450	Thermofisher	Clone: 4B10; RRID: AB_2784727; Cat#48-5825-82
BB790 Mouse Anti-IRF4	BD Biosciences custom	Clone: Q9-343
Biotin anti-human IgG Fc Antibody	Biolegend	Clone: HP6017; RRID:AB_11150771; Cat#409307
Chemicals, peptides, and recombinant proteins
Fixable Viability Dye eFluor™ 780	eBioscience	Lot#2290917; Cat#65-0865-14
BD brilliant stain buffer	BD Biosciences	RRID: AB_2869750; Cat#563794; Lot: 0119708
Biotinylated mutant Cal09-HA Haemagglutinin	Gifted by Adam Wheatley	N/A
Streptavidin-Biotinylated HRP Complex	Amersham	Cat#RPM1051; Batch: 195367
APC-streptavidin	Thermofisher	Cat#S868
PE-streptavidin	Thermofisher	Cat#S866
Trypan Blue solution	Sigma-Aldrich	Cat#T8154
Receptor Destroying Enzyme	Denka Seiken	N/A
Hemagglutinin HA (A/California/06/2009)	eEnzyme	GenBank accession: ACP41935; Cat#IA-11SW-005P
Critical commercial assays
Protease Inhibitor Cocktail Set I	Merck	Cat#539131
MagniSort™ Human B Cell Enrichment Kit	eBioscience	Cat#8804-6867-74; Lot: 2345066
SMART-Seq® HT Kit	Takara Clontech	Cat#634436
Qubit dsDNA HS assay kit	Life Technologies	Cat#Q32854
Nextera XT DNA Library Preparation Kit	Illumina	Cat#FC-131-1096
Nextera Index Kit v2 Set A	Illumina	Cat#FC-131-2001
eBioscience Foxp3/Transcription Factor Fixation/Permeabilisation Staining buffer set	ThermoFisher	Cat#00-5523-00
KAPA Library Quantification Kits - Complete Kit (universal)	Kapa Biosystems	Cat#KK4824
Deposited data
Raw sequence reads from Turner et al. (2020)	NCBI Gene Expression Omnibus (GEO) database	GEO: GSE148633
Monaco et al. dataset	Monaco et al. 2019	N/A
R code for the SMART-Seq gene expression and BCR analyses, 10×/Seurat analyses, and phenotypic data	github repository: https://github.com/lintermanlab/B_flu_scRNAseq	https://doi.org/10.5281/zenodo.7116358
Single cell RNA sequencing data (SMART-Seq)	This paper; deposited in GEO. (https://www.ncbi.nlm.nih.gov/geo/)	GEO: GSE167823
Singel cell RNA sequencing data of paired blood and lymph node sampling (10×)	Turner et al., 2020; deposited in GEO	GEO: GSE148633
Software and algorithms
FlowJo v10.8	Treestar	https://www.flowjo.com/
R v3.6.1 & R v4.0.0	www.r-project.org	N/A
RStudio v1.2.5001	www.rstudio.com	N/A
miloR v0.99.18	https://www.bioconductor.org/packages/release/bioc/html/miloR.html	Dann et al., 2022
trimgalore v 0.6.6	https://github.com/FelixKrueger/TrimGalore	N/A
HISAT2 v 2.1.0	http://daehwankimlab.github.io/hisat2/	Kim et al., 2015
Rsubread v2.0.0	https://bioconductor.org/packages/release/bioc/html/Rsubread.html	Liao et al., 2019
Bioconductor	https://bioconductor.org	Huber et al., 2015
Scater v1.14.5	https://bioconductor.org/packages/release/bioc/html/scater.html	McCarthy et al., 2017
Scran v1.14.5	https://bioconductor.org/packages/release/bioc/html/scran.html	Lun et al., 2016
SingleCellExperiment v1.8.0	https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html	Amezquita et al., 2020
Igraph v1.2.4.2	https://igraph.org	Csardi and Nepusz, 2006
SingleR v1.0.6	https://bioconductor.org/packages/release/bioc/html/SingleR.html	Aran et al., 2019
destiny v3.0.1	https://bioconductor.org/packages/release/bioc/html/destiny.html	Angerer et al., 2015
edgeR v3.28.0	https://bioconductor.org/packages/release/bioc/html/edgeR.html	Robinson et al., 2010
flowCore v1.52.1	https://bioconductor.org/packages/release/bioc/html/flowCore.html	Ellis et al., 2019
ggcyto v1.18.0	https://bioconductor.org/packages/release/bioc/html/ggcyto.html	Van et al., 2018
immunarch v 0.6.6	https://immunarch.com	Nazarov et al., 2020
Seurat R package v3.2.2	https://satijalab.org/seurat/index.html	Stuart et al., 2019
Rmarkdown	N/A	Allaire et al., 2021; Xie et al., 2018, 2020
VDJPuzzle	https://bitbucket.org/kirbyvisp/vdjpuzzle2/src/master/	Rizzetto et al., 2018
SRAtoolkit v2.10.8	https://github.com/ncbi/sra-tools/	N/A
cellranger count v5.0.0	10× Genomics	N/A
cellranger vdj v5.0.0	10× Genomics	N/A
Immcantation suite	https://immcantation.readthedocs.io/en/stable/	Gupta et al., 2015
TSNE and heatmap analysis	R v4.1.2	Pasciuto et al., 2020
Other
Chicken Blood Cells (Adult) in Alsever’s	TCS Biosciences	Cat#FB010AP
RPMI 1640 Medium	Life Technologies	Cat#21875-091
Heat Inactivated Fetal Bovine Serum	Sigma-Aldrich	Cat#F9665
Penicillin-Streptomycin	Life Technologies	Cat#15140-122
TWEEN® 20	Sigma-Aldrich	Cat#P1379
Histopaque®-1077	Sigma-Aldrich	Cat#10771
L-Glutamine solution	Sigma-Aldrich	Cat#G7513
DMSO	Sigma-Aldrich	Cat#34869
AMPure XP beads	Beckman Coulter	Cat#A63881