KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Armenian hamster anti-mouse CD40L (clone MR-1) | BioXCell | Cat# BE0017 |
| Rat anti-mouse ICAM-1 (clone YN1/1.7.4) | BioXCell | Cat# BE0020 |
| Polyclonal armenian hamster IgG | BioXCell | Cat# BE0091 |
| Rat IgG2b isotype control | BioXCell | Cat# BE0090 |
| Rat anti-mouse CD16/CD32 (Fc block) | BD Biosciences | Cat# 553142 |
| Rat eFluor506 anti-B220 | ThermoFisher Scientific | Cat# 69–0452 |
| Rat APC anti-CD38 | ThermoFisher Scientific | Cat# 17–0381 |
| Rat PE anti-CXCR4 | ThermoFisher Scientific | Cat# 12–9991 |
| Rat APC anti-CD4 | ThermoFisher Scientific | Cat# 17–0041 |
| Mouse PerCP-Cy5.5 anti-CD45.1 | ThermoFisher Scientific | Cat# 45–0453 |
| Mouse PE-Cy7 anti-CD45.2 | ThermoFisher Scientific | Cat# 25–0454 |
| Armenian hamster FITC anti-PD-1 | ThermoFisher Scientific | Cat# 11–9985 |
| Rat APC anti-B220 | BD Biosciences | Cat# 553092 |
| Rat BV786 anti-B220 | BD Biosciences | Cat# 563894 |
| Hamster PE anti-FAS | BD Biosciences | Cat# 554258 |
| Hamster PE-Cy7 anti-FAS | BD Biosciences | Cat# 557653 |
| Hamster BV421 anti-FAS | BD Biosciences | Cat# 562633 |
| Rat FITC anti-CD38 | BD Biosciences | Cat# 558813 |
| Rat BV395 anti-CD38 | BD Biosciences | Cat# 740245 |
| Rat PE-Cy7 anti-CD86 | BD Biosciences | Cat# 560582 |
| Rat BV421 anti-CD86 | BD Biosciences | Cat# 564198 |
| Rat biotin anti-CXCR4 | BD Biosciences | Cat# 551968 |
| Rat biotin anti-CXCR5 | BD Biosciences | Cat# 551960 |
| Rat PE anti-IgD | BD Biosciences | Cat# 558597 |
| Rat BV510 anti-IgD | BD Biosciences | Cat# 563110 |
| Rat APC anti-IgG1 | BD Biosciences | Cat# 560089 |
| Rat BV421 anti-IgG1 | BD Biosciences | Cat# 562580 |
| Rat BUV737 anti-CD138 | BD Biosciences | Cat# 564430 |
| Rabbit AF647 anti-active caspase-3 | BD Biosciences | Cat# 560626 |
| Mouse BV421 anti-Ki67 | BD Biosciences | Cat# 562899 |
| Rat BUV395 anti-BAFF-R | BD Biosciences | Cat# 742871 |
| Rat BV650 anti-ICAM-2 | BD Biosciences | Cat# 740470 |
| Mouse BV711 anti-Ly108 | BD Biosciences | Cat# 740823 |
| Mouse AF488 anti-EZH2 | BD Biosciences | Cat# 562479 |
| Rat BV421 anti-CD35 | BD Biosciences | Cat# 740029 |
| Rat APC-Cy7 anti-B220 | BioLegend | Cat# 103224 |
| Rat PE anti-B220 | BioLegend | Cat# 103208 |
| Rat APC-Cy7 anti-CD38 | BioLegend | Cat# 102728 |
| Rat PerCP-Cy5.5 anti-GL7 | BioLegend | Cat# 144610 |
| Mouse PerCP-Cy5.5 anti-FAS | BioLegend | Cat# 152610 |
| Rat APC anti-CD86 | BioLegend | Cat# 105012 |
| Rat biotin anti-CD83 | BioLegend | Cat# 121504 |
| Rat PE-Cy7 anti-CD138 | BioLegend | Cat# 142514 |
| Rat BV421 anti-CD138 | BioLegend | Cat# 142508 |
| Mouse APC-Cy7 anti-CD45.2 | BioLegend | Cat# 109824 |
| Rat PerCP-Cy5.5 anti-ICAM-1 | BioLegend | Cat# 116123 |
| Mouse AF594 anti-CD45.1 | BioLegend | Cat# 110750 |
| Mouse AF647 anti-CD45.2 | BioLegend | Cat# 109817 |
| Rat AF488 anti-IgD | BioLegend | Cat# 405717 |
| Mouse anti-human CD21 (clone 2G9) | Cell Marque | Cat# 121M |
| Rabbit AF647 anti-H3K27me3 | Cell Signaling | Cat# 12158 |
| Goat HRP-conjugated anti-mouse IgG1 | SouthernBiotech | Cat# 1070–05 |
| Goat HRP-conjugated anti-mouse IgM | SouthernBiotech | Cat# 1020–05 |
| Mouse immunoglobulin panel (IgG1, IgG2a, IgG2b, IgG3, IgA, IgM) | SouthernBiotech | Cat# 5300–01 |
| Goat anti-mouse Kappa | SouthernBiotech | Cat# 1050–01 |
| Goat anti-mouse Lambda | SouthernBiotech | Cat# 1060–01 |
| Rabbit H3K27me3 (for ChIP) | Cell Signaling | Cat# 9733 |
| Biological Samples | ||
| Sheep red blood cells | Cocalico Biologicals | Cat# 20–1334A |
| Tissue microarrays of 232 primary diagnosed FL | Kridel et al., 2016 | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| NP-OVAL | Biosearch Technologies | Cat# N-5051 |
| NP-CGG | Biosearch Technologies | Cat# N-5055C |
| NP-KLH | Biosearch Technologies | Cat# N-5060 |
| Alum adjuvant | ThermoFisher Scientific | Cat# 77161 |
| mLTβR (recombinant mouse Lymphotoxin beta R/TNFRSF3 Fc Chimera) | R&D Systems | Cat# 1008-LR |
| PE NP | Biosearch Technologies | Cat# N-5070 |
| NIP-haptenated FITC | M. Shlomchik lab; Anderson et al., 2007 | N/A |
| Peptide OVA323–339 | MBL International | Cat# TS-M703 |
| Biotinylated Peanut Agglutinin (PNA) | Vector Laboratories | Cat# B-1075 |
| APC streptavidin | BioLegend | Cat# 405207 |
| PE-Cy7 streptavidin | ThermoFisher Scientific | Cat# 25–4317 |
| AF488 streptavidin | BioLegend | Cat# 405235 |
| AF555 streptavidin | Invitrogen | Cat# S32355 |
| NP-BSA, ratio >20 | Biosearch Technologies | Cat# N-5050H |
| NP-BSA, ratio 1–4 | Biosearch Technologies | Cat# N-5050XL |
| Critical Commercial Assays | ||
| Cytofix/Cytoperm Fixation/Permeabilization Kit | BD Biosciences | Cat# 554714 |
| Phosflow Perm Buffer III | BD Biosciences | Cat# 558050 |
| Annexin V binding buffer | BD Biosciences | Cat# 556454 |
| APC conjugated Annexin V | BD Biosciences | Cat# 550475 |
| CaspGLOW Fluorescein Active Caspase Staining Kit (FITC-VAD-FMK pan-caspase inhibitor) | BioVision | Cat# K180 |
| CD45R (B220) magnetic microbeads | Miltenyi Biotec | Cat# 130–049-501 |
| CellTrace CFSE Cell Proliferation Kit | Life Technologies | Cat# C34554 |
| CellTrace Violet Cell Proliferation Kit | Life Technologies | Cat# C34557 |
| Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit | 10X Genomics | Cat# 1000128 |
| TruSeq RNA Library Preparation Kit v2 | Illumina | Cat# RS-122–2001 |
| True MicroChIP & MicroPlex Library Preparation Kit | Diagenode | Cat# C01010131 |
| Deposited Data | ||
| Raw sequencing data | This manuscript | GEO: GSE138037 |
| FL RNA-seq | Ortega-Molina et al, 2015 | SRA: SRP056293 |
| FL RNA microarray | Green et al., 2015 | GEO: GSE56311 |
| Experimental Models: Organisms/Strains | ||
| Mouse: Ezh2Y641F: Ezh2(Y641F)fl knock-in | Béguelin et al., 2016 | N/A |
| Mouse: Cγ1-cre: B6.129P2(Cg)-Ighg1tm1(cre)Cgn/J | The Jackson Laboratory | Stock# 010611 |
| Mouse: C57BL/6J | The Jackson Laboratory | Stock# 000664 |
| Mouse: B6.SJL-PtprcaPepcb/BoyJ | The Jackson Laboratory | Stock# 002014 |
| Mouse: Rag1 KO: B6.129S7-Rag1tm1Mom/J | The Jackson Laboratory | Stock# 002216 |
| Mouse: R26-lox-stop-lox-YFP: B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J | The Jackson Laboratory | Stock# 006148 |
| Mouse: OT-II: B6.Cg-Tg(TcraTcrb)425Cbn/J | The Jackson Laboratory | Stock# 004194 |
| Mouse: R26R-Confetti: Gt(ROSA)26Sortm1(CAG-Brainbow2.1)Cle/J | The Jackson Laboratory | Stock# 013731 |
| Mouse: GFP-Myc: B6;129-Myctm1Slek/J | The Jackson Laboratory | Stock# 021935 |
| Mouse: R26-Fucci2aR | Mort et al., 2014 | N/A |
| Oligonucleotides | ||
| Primers used for qChIP, see Table S3 | This manuscript | N/A |
| Primers used for RT-qPCR, see Table S3 | This manuscript | N/A |
| Primers for IgG1 and IgM PCR and sequencing (Figure 8A) | Tiller et al., 2009 | N/A |
| Software and Algorithms | ||
| FlowJo | Becton Dickinson | Version 10.5.3 |
| Fiji (ImageJ) | Schindelin et al., 2012 | http://fiji.sc/ |
| Chromium Single Cell Gene Expression | 10X Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software |
| Seurat | Stuart et al., 2019 | https://satijalab.org/seurat/ |
| UMAP | McInnes et al., 2018 | https://umap-learn.readthedocs.io/en/latest/ |
| Slingshot and dyno package | Saelens et al., 2019; Street et al., 2018 | https://dynverse.org/dyno/reference/index.html |
| GSEA2 v2.0.13 | Broad Institute | http://software.broadinstitute.org/gsea/index.jsp |
| CASAVA | Illumina | Version 1.8.2 |
| Trim Galore! v0.4.1 | Babraham Institute | www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| STAR transcriptome aligner v2.5.1b | Dobin et al., 2013 | http://code.google.com/p/rna-star/ |
| featureCounts | Liao et al., 2014 | http://subread.sourceforge.net |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| PAGE algorithm | Goodarzi et al., 2009 | https://github.com/goodarzilab/PAGE |
| CompChIPseq algorithm | Blanco et al., 2019 | N/A |
| DeepTools | Ramirez et al., 2014 | https://deeptools.readthedocs.io/en/develop/content/example_gallery.html |
| Denstrip R | Jackson et al., 2008 | https://cran.r-project.org/web/packages/denstrip/index.html |
| SICER algorithm | Xu et al., 2014 | http://home.gwu.edu/~wpeng/Software.htm |
| Skyline | MacLean et al., 2010 | https://skyline.ms/wiki/home/software/Skyline/page.view?name=default |
| pRESTO v0.5.10 | Vander Heiden et al., 2014 | https://presto.readthedocs.io/en/stable/ |
| USearch v7.0.1090 | Edgar, 2010 | http://www.drive5.com/usearch |
| IgBLAST v1.13.0 | Ye et al., 2013 | http://www.ncbi.nlm.nih.gov/igblast/ |
| Change-O v0.4.5 | Gupta et al., 2015; Gupta et al., 2017 | https://changeo.readthedocs.io |
| Alakazam v0.3.0 | Gupta et al., 2015; Gupta et al., 2017 | https://alakazam.readthedocs.io |
| SHazaM v0.2.0 | Yaari et al., 2013 | https://shazam.readthedocs.io |
|
dnapars v3.697; Phylogeny Inference Package, v3.6a3 |
Felsenstein J., 2002 | http://evolution.genetics.washington.edu/phylip.html |
| IgPhyML v1.1.1 | Hoehn et al., 2019 | https://igphyml.readthedocs.io |
| ggtree v1.16.0 | Yu et al., 2017; Yu et al., 2018 | https://guangchuangyu.github.io/software/ggtree/ |
| Other | ||
| Sequence processing and analysis scripts of single cell immunoglobulin somatic hypermutation | This manuscript | https://bitbucket.org/kleinstein/melnick_gcb_scripts |