KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-CD19 BV785 (clone 1D3) | BD Bioscience | Cat#563333; RRID: AB_2738141 |
| anti-B220 BV785 (clone RA3–6B2) | BioLegend | Cat#103246; RRID: AB_2563256 |
| anti-IgD FITC (clone 11–26c.2a) | BioLegend | Cat#405704; RRID: AB_394859 |
| anti-IgD Alexa Fluor 647 (clone 11–26c.2a) | BioLegend | Cat#405708; RRID: AB_893528 |
| anti-IgD Pacific Blue (clone 11–26c.2a) | BioLegend | Cat#405712; RRID: AB_1937244 |
| anti-IgD BV605 | BD Bioscience | Cat#563003; RRID: AB_2737944 |
| anti-IgD PerCP/Cy5.5 | BioLegend | Cat#405710; RRID: AB_1575113 |
| anti-GL-7 (Ly-77) Pacific Blue (clone GL7) | BioLegend | Cat#144614; RRID: AB_2563292 |
| anti-GL-7 (Ly-77) FITC (clone GL7) | BioLegend | Cat#144604; RRID: AB_2561697 |
| anti-CD95 PE-CY7 (clone Jo2) | BD Bioscience | Cat#557653; RRID: AB_396768 |
| anti-CD45.1 PERCP-CY5.5 (clone A20) | Tonbo | Cat#65–0453-U100 |
| anti-CD45.1 BV605 (clone A20) | BioLegend | Cat#110738; RRID: AB_2562565 |
| anti-CD45.2 BV605 (clone 104) | BioLegend | Cat#109841; RRID: AB_2563485 |
| anti-Ephrin-B1 Biotin (polyclonal) | R&D | Cat#BAF473; RRID: AB_2293418 |
| anti-CXCR4 Biotin (clone 2B11) | BD Bioscience | Cat#551968; RRID: AB_394307 |
| anti-CD86 BV605 | Biolegend | Cat#105037; RRID: AB_11204429 |
| anti-IgG1 FITC (clone RMG1–1) | BioLegend | Cat#406606; RRID: AB_493293 |
| anti-IgG1 APC | BioLegend | Cat#406610; RRID: AB_10696420 |
| anti-CD138 BV421 (clone 281–2) | BioLegend | Cat#142508; RRID: AB_11203544 |
| anti-CD138 BV711 (clone 281–2) | BD Bioscience | Cat#563193; RRID: AB_2631190 |
| anti-CD98 BV711 | BD Bioscience | Cat#745466; RRID: AB_2743009 |
| anti-CD73 PERCP-CY5.5 (clone TY/11.8) | BioLegend | Cat#127214; RRID: AB_11219403 |
| anti-gp38 APC (clone 8.1.1) | BioLegend | Cat#127410; RRID: AB_10613649 |
| anti-CD31 PE (clone MEC 13.3) | BD Biosciences | Cat#553373; RRID: AB_394819 |
| anti-CD31 PE-Cy7 (clone MEC 13.3) | BioLegend | Cat#102417; RRID: AB_830756 |
| anti-Epcam BV711 | BioLegend | Cat#118233; RRID: AB_2632775 |
| anti-CD21/35 pacific Blue | BioLegend | Cat#123414; RRID: AB_2085158 |
| Streptavidin BV711 | BD Bioscience | Cat#563262; RRID: AB_2869478 |
| anti-CD79b FITC | BD Bioscience | Cat#555303; RRID: AB_395717 |
| anti-CD23 Alexa Fluor 488 | BioLegend | Cat#101609; RRID: AB_493362 |
| anti-CD23 Alexa Fluor 647 | BioLegend | Cat#101612; RRID: AB_2103038 |
| anti-CD72 | BD Bioscience | Cat#550268; RRID: AB_393565 |
| anti-IL4ra PE (Clone mIL4R-M1) | BD Bioscience | Cat#552509; RRID: AB_394407 |
| anti-IL4 (clone 11B11) | Bio X cell | Cat#BE0045; RRID: AB_1107707 |
| Fixable Viability Dye eFluor780 | eBioscience | Cat#65–0865-14 |
| anti-CD38 PE-Cy7 | BioLegend | Cat#102718; RRID: AB_2275531 |
| anti-CD38 FITC | BioLegend | Cat# 102705; RRID: AB_312926 |
| anti-CD196 Alexa Fluor 647 | BD Bioscience | Cat#557976; RRID: AB_2228793 |
| anti-Ki67 Alexa Fluor 647 | BD Bioscience | Cat#558615; RRID: AB_647130 |
| anti-Bcl-6 Alexa Fluor 647 | BD Bioscience | Cat#561525; RRID: AB_10898007 |
| anti-pStat6 (Tyr641) (46H1L12) | Thermo Fisher Scientific | Cat# 700247; RRID: AB_2532305 |
| Rabbit anti-Tmem119 | B. Barres | Bennett et al., 2016 |
| AS20/anti-CD45.1-OVA | This paper | NA |
| Bacterial and virus strains | ||
| Biological samples | ||
| Chemicals, peptides, and recombinant proteins | ||
| Lipopolysaccharides (Escherichia coli, serotype O111:B4) | Sigma | Cat# L2630–25MG |
| NP-CGG | Biosearch Technologies | Cat#N-5055C-5 |
| NP-KLH | Biosearch Technologies |
Cat#N-5060 |
| NP-PE | Biosearch Technologies | Cat#N-5070–1 |
| Collagenase IV | Worthington Biochemical | Cat#LS004188 |
| DNase I, bovine pancreas (single cell stromal cell analysis) | Sigma-Aldrich | Cat#DN25 |
| EdU (5-ethynyl-2’-deoxyuridine) | Setareh Biotech | Cat#7180 |
| mLTbR-huIgG1 (LTbR-Fc) | J. Browning | N/A |
| Aluminium hydroxide gel | Invivogen | Cat#vac-alu-250 |
| Murine recombinant IL-4 | PeproTech | Cat#214–14 |
| Critical commercial assays | ||
| Chromium Single Cell 5′ Library & Gel Bead Kit | 10x Genomics | Cat#1000014 |
| Chromium i7 Multiplex Kit | 10x Genomics | Cat#120262 |
| Chromium Single Cell A Chip Kit | 10x Genomics | Cat#1000151 |
| Chromium Single Cell 5′ Library Construction Kit | 10x Genomics | Cat#1000020 |
| Chromium Single Cell V(D)J Enrichment Kit, Mouse B Cell | 10x Genomics | Cat#1000072 |
| Click-iT Plus EdU Alexa Fluor 647 Flow Cytometry Assay Kit 100 Tests | Invitrogen | Cat#C10635 |
| Lipofectamine 2000 Transfection Reagent | Thermo Fisher Scientific | Cat# 11668500 |
| Deposited data | ||
| 10x single cell RNA-seq data | This paper | GSE180920 |
| BCR heavy chain sequencing data | This paper | Table S4 |
| IL4 incubation RNA-seq data | Mokada-Gopal et al., 2017 | GSE84075 |
| Spleen stromal cell single cell RNA-seq data | Cheng et al., 2019 | E-MTAB-7703, E-MTAB-7094 |
| NP-specific high- and low-affinity GC B cell RNA-seq data | Shinnakasu et al., 2016 | GSE73729 |
| Pre plasma cell RNA-seq data | Ise et al., 2018 | GSE109732 |
| Post GC B cell RNA-seq data | Laidlaw et al., 2017 | GSE89897 |
| Pre memory B cell RNA-seq data | Wang et al., 2017 | GSE85018 |
| Experimental models: Cell lines | ||
| Platinum-E (Plat-E) Retroviral Packaging Cell Line | Gift from S. Schwab | N/A |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6J | The Jackson Laboratory | JAX: 000664 |
| Mouse: B6.SJL-Ptprca Pepcb/BoyJ | The Jackson Laboratory | JAX: 002014 |
| Mouse: Rosa26-LSL-Cas9 | The Jackson Laboratory | JAX: 024857 |
| Mouse: Il4ra−/− | The Jackson Laboratory | JAX:003514 |
| Mouse: Cγ1Cre/+ | The Jackson Laboratory | JAX: 010611 |
| Mouse: B6.129S4-Il2rgtm1Wjl/J | The Jackson Laboratory | JAX:003174 |
| Mouse: Aicdatm1Hon | Muramatsu et al., 2000 | MGI: 2156156 |
| Mouse: Blimp1Gfp/+ | Kallies et al., 2004 | MGI: 3510704 |
| Mouse: Il4raf/f | Herbert et al., 2004 | N/A |
| Mouse: Ccl19Cre/+ | Chai et al., 2013 | MGI: 5526991 |
| Mouse: CD21Cre/+ | Kraus et al., 2004 | MGI: 3047571 |
| Mouse: S1pr2CreERT2/+ | Shinnakasu et al., 2016 | MGI: 6435090 |
| Mouse: Stat6−/− | Takeda et al., 1996 | MGI: 1888385 |
| Mouse: S1pr2Venus/+ | Moriyama et al., 2014 | N/A |
| Oligonucleotides | ||
| Il4ra sgRNA 1 (5’-CAAAATCAGACAGCCCACAG-3’) | This paper | N/A |
| Il4ra sgRNA 2 (5’-GATGTAGTCAGAGAAGCAGG-3’) | This paper | N/A |
| Recombinant DNA | ||
| pMCP-BFP | Kotov et al., 2019 | N/A |
| Software and algorithms | ||
| GraphPad Prism | GraphPad Software |
http://www.graphpad.com/scientific-software/prism/ RRID: SCR_002798 |
| Fiji | NIH |
http://fiji.sc/ RRID: SCR_002285 |
| R v3.6.2 | R Foundation for Statistical Computing | https://www.r-project.org/ |
| Cell Ranger v3.1.0 | 10x Genomics |
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger RRID: SCR_017344 |
| Seurat v3.1.1 | Satija Lab |
http://satijalab.org/seurat/ RRID: SCR_007322 |
| Scanpy v1.4.6 | Theis Lab |
https://icb-scanpy.readthedocs-hosted.com/en/stable/ RRID: SCR_018139 |
| ScVelo v0.1.25 | Theis Lab |
https://scvelo.readthedocs.io/index.html RRID: SCR_018168 |
| Velocyto v0.17 | velocyto-team |
http://velocyto.org/ RRID: SCR_018167 |
| LoomR v0.2.1.9 | Satija Lab | https://github.com/mojaveazure/loomR |
| loompy v3.0 | Linnarsson Lab |
http://loompy.org/ RRID: SCR_016666 |
| Monocle 2 | Trapnell lab |
http://cole-trapnell-lab.github.io/monocle-release/docs/ RRID: SCR_016339 |
| VISION v1.1.0 | Yosef Lab | https://yoseflab.github.io/VISION/news/index.html |
| IgBLAST V1.14.0 | NCBI |
https://ncbi.github.io/igblast/rel/Release-notes.html RRID: SCR_002873 |
| Immcantation | Kleinstein Lab | https://immcantation.readthedocs.io/en/stable/index.html |
| Plotly Python Open Source Graphing Library v4.5.3 | Plotly |
https://github.com/plotly/plotly.py/ RRID: SCR_013991 |
| RStudio | RStudio |
https://www.rstudio.com/products/rstudio/ RRID: SCR_000432 |
| GSEA v4 for Linux | GSEA team |
https://www.gsea-msigdb.org/gsea/index.jsp RRID: SCR_003199 |
| Weblogo 3 | Crooks et al., 2004 |
http://weblogo.threeplusone.com/ RRID: SCR_010236 |
| Flowjo | Treestar |
https://www.flowjo.com/ RRID: SCR_008520 |
| Other | ||