Reagent/resource	Reference or source	Identifier or catalog number
Experimental models
Details described in Table EV1
Antibodies
PanCK(C11)	Cell Signaling Technology	Cat # 4545
CD3(BP6027)	Biolynx	Cat # BX50022
CD56(123C3)	Cell Signaling Technology	Cat # 3576
CD68(BP6036)	Biolynx	Cat # BX50031
CD20(E7B7T)	Cell Signaling Technology	Cat # 48750
BCL6(EPR11410‐43)	Abcam	Cat # ab172610
CD38(EPR4106)	Abcam	Cat # ab108403
CD8(1G2B10)	Proteintech	Cat # 66868‐1‐Ig
CD4(2H4A2)	Proteintech	Cat # 67786‐1‐Ig
CD4(EPR6855)	Abcam	Cat # ab133616
PD‐1(10377‐H08H)	Sinobiological	Cat # 10377‐MM23
CXCL13(EPR23400‐92)	Abcam	Cat # ab246518
CD14(4B4F12)	Abcam	Cat # ab182032
Ki‐67(BP6045)	Biolynx	Cat # BX50040
HRP‐labeled Goat Anti‐ RabbitIgG	Yuanxi Bio	Cat # A10012‐60
Goat Anti‐Mouse IgG H&L (HRP)	Abcam	Cat # ab205719
Chemicals, enzymes and other reagents
MACS Tissue Storage Solution	Miltenyi Biotec	Cat # 130‐100‐008
RPMI medium	Gibco	Cat # C11875500BT
Fetal bovine serum	Gibco	Cat # A3161001C
Trypsin	ThermoFisher Scientific	Cat # 25200072
Collagenase type IV	Worthington	Cat # LS004186
Collagenase type I	Worthington	Cat # LS004194
Dispase II	Roche	Cat # 4942078001
Red blood cell lysis buffer	Gibco	Cat # A1049201
DAB substrate kit	Abcam	Cat # ab64238
Bovine serum albumin (BSA)	Sigma‐Aldrich	Cat # A9647
Tris buffered saline with Tween 20 (TBST)	ThermoFisher Scientific	Cat # 37543
4′‐6′‐diamidino‐2‐phenylindole (DAPI)	Sigma‐Aldrich	Cat # D9542
Software
Cell Ranger toolkit (version 5.0.0)	10× Genomics	https://support.10xgenomics.com
MAESTRO v 1.5.1	Wang et al (2020)	https://github.com/liulab‐dfci/MAESTRO
MAESTRO v 1.5.0	Wang et al (2020)	https://github.com/liulab‐dfci/MAESTRO
DoubletFinder	McGinnis et al (2019)	https://github.com/ddiez/DoubletFinder
Python 3	N/A	www.python.org
R 3.5.0	R‐Project	https://cran.r‐project.org/mirrors.html
Seurat v2.3.4	Satija et al (2015)	https://satijalab.org/seurat/
ClusterProfiler v 3.18.1	Yu et al (2012)	https://guangchuangyu.github.io/software/clusterProfiler/
scCODA	Buttner et al (2021)	https://github.com/theislab/scCODA
TRUST4 v1.0.5.1	Song et al (2021)	https://github.com/milaboratory/mixcr‐rna‐seq‐paper
VDJmatch v1.2.2	Shugay et al (2018)	https://vdjdb.cdr3.net
ggplot2	Hadley Wickham et al (2016)	https://cran.r‐project.org/web/packages/ggplot2/index.html
ggpubr v0.4	R‐Project	https://cran.r‐project.org/web/packages/ggpubr/index.html
CopyKat	Gao et al (2021)	https://github.com/navinlabcode/copykat
GSVA v1.38.2	Hanzelmann et al (2013)	https://www.bioconductor.org/packages/release/bioc/html/GSVA.html
CellPhoneDB v0.22	Efremova et al (2020)	www.cellphonedb.org
CellChat v1.1.0	Jin et al (2021)	http://www.cellchat.org/
Monocle2 v4.0.5	Qiu et al (2017)	https://cole‐trapnell‐lab.github.io/monocle‐release/
GraphPad Prism 7.0	GraphPad	https://www.graphpad.com/
Halo10 software	Indica Labs	https://indicalab.com/halo/
Other
Illumina NexSeq 500	Illumina
Chromium Next GEM Single Cell 5′ Kit v1.1	10× Genomics	PN‐1000165
PanoVIEW VS200 slide scanner	Panovue
TSA 5‐color kit	Yuanxi Bio	Cat # H‐D110051
PDOne 5‐plex TSA‐RM kit	Panovue	Cat # 10144100100