REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
1X Phosphate-Buffered Saline	Thermo Fisher	Cat#20012-019
MACS BSA Stock Solution	Miltenyi Biotec	Cat#130-091-376
Nuclease free water	Ambion	Cat#AM9939
Hibernate-A medium	Gibco	Cat#A1247501
RNAse Inhibitor	Roche	Cat#3335402001
Trypan blue	Fischer Scientific	Cat#15250-061
Digitonin 5%	Fischer Scientific	Cat#10636033
NaCl 5 M	Ambion	Cat#AM9759
MgCl2 1M	Ambion	Cat#AM9530G
Nonidet P40	Sigm-Aldrich	Cat#74385
Tween-20	Thermo Fisher	Cat#85114
Tris-HCl 1M pH 7.5	Thermo Fisher	Cat#15567027
Critical commercial assays
Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1	10x Genomics	Cat#1000121
Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1	10x Genomics	Cat#1000175
Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1	10x Genomics	Cat#1000165
Chromium Single Cell V(D)J Enrichment Kit, Human T Cell	10x Genomics	Cat#1000005
Chromium Single Cell V(D)J Enrichment Kit, Human B Cell	10x Genomics	Cat#1000016
Visium Spatial Tissue Optimization Slide & Reagent Kit	10x Genomics	Cat#1000193
Visium Spatial Gene Expression Slide & Reagent Kit	10x Genomics	Cat#1000184
Agilent High Sensitivity DNA Kit	Agilent	Cat#5067-4626
Agilent RNA 6000 Pico Kit	Agilent	Cat#5067-1513
RNeasy Plus Micro kit	Qiagen	Cat#74034
AMPure XP Bead-Based Reagent	Beckman Coulter	Cat#A63881
Software and algorithms
Cellranger-atac v1.2	CellRanger ATAC (10X Genomics)	https://support.10xgenomics.com/single-cell-atac/software/overview/welcome
Cellranger v4.0.0	CellRanger (10X Genomics)	https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome
Cellranger-arc v1.0	CellRanger ARC (10X Genomics)	https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/overview/welcome
Cellranger-multi v6.0.1	CellRanger multi (10X Genomics)	https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/multi
Spaceranger v1.1.0	10X Genomics	https://support.10xgenomics.com/spatial-gene-expression/software/overview/welcome
Seurat v3.2.0 and v4.1.0	Hao et al.18	https://satijalab.org/seurat/
Signac v1.1.0	Stuart et al.106	https://satijalab.org/signac/
Harmony v1.0	Korsunsky et al.107	https://github.com/immunogenomics/harmony
clusterProfiler v4.3.4	Wu et al.108	https://yulab-smu.top/biomedical-knowledge-mining-book/
UCell v1.2.0	Andreatta and Carmona109	https://bioconductor.org/packages/release/bioc/html/UCell.html
MACS2 v2.2.7.1	Zhang et al.110	https://github.com/macs3-project/MACS
ChromVar v1.1.0	Schep et al.111	http://www.bioconductor.org/packages/release/bioc/html/chromVAR.html
Cicero v1.3.4	Pliner et al.112	http://cole-trapnell-lab.github.io/cicero-release
pySCENIC v0.10.3	Van de Sande et al.24	https://pyscenic.readthedocs.io/en/latest/
SCENIC+	Bravo González-Blas et al.25	https://scenicplus.readthedocs.io/
pycisTopic	Bravo González-Blas et al.25	https://github.com/aertslab/pycisTopic
pycistarget	Bravo González-Blas et al.25	https://github.com/aertslab/pycistarget
Vireo v0.5.0	Huang et al.113	https://github.com/single-cell-genetics/vireo
cellsnp-lite v1.2.0	Huang and Huang114	https://github.com/single-cell-genetics/cellsnp-lite
Scirpy v0.7.0	Sturm et al.115	https://github.com/scverse/scirpy
SPOTlight v0.1.7	Elosua-Bayes et al.116	https://www.bioconductor.org/packages/release/bioc/html/SPOTlight.html
Rmagic v2.0.3	van Dijk et al.117	https://github.com/KrishnaswamyLab/MAGIC
SPATA2 v0.1.0	Kueckelhaus et al.118	https://github.com/theMILOlab/SPATA2
LISI v1.0	Korsunsky et al.107	https://github.com/immunogenomics/LISI
Scrublet v0.2.1	Wolock et al.119	https://github.com/swolock/scrublet
ChipSeeker v1.34.1	Wang et al.120	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html
scCODA v0.1.9	Büttner et al.98	https://pypi.org/project/scCODA/
Infercnv	Tirosh et al.101	https://github.com/broadinstitute/inferCNV/wiki
ComplexHeatmap v2.14.0	Gu121	https://jokergoo.github.io/ComplexHeatmap-reference/book/
R	R core	https://www.r-project.org
Python	Python Software Foundation	https://www.python.org
Custom Shiny App to annotate clusters	This paper	https://singlecellgenomics-cnag-crg.shinyapps.io/Annotation/
Custom Shiny App to annotate histology slides	This paper	https://github.com/Single-Cell-Genomics-Group-CNAG-CRG/shiny-pathology
HCATonsilData	This paper	https://bioconductor.org/packages/release/data/experiment/html/HCATonsilData.html
SLOcatoR	This paper	https://github.com/massonix/SLOcatoR
iSee instance	This paper	http://shiny.imbei.uni-mainz.de:3838/iSEE_TonsilDataAtlas/
Azimuth app and reference	This paper	https://azimuth.hubmapconsortium.org/references/#Human%20-%20Tonsil%20v2
Code and vignettes	This paper	https://github.com/Single-Cell-Genomics-Group-CNAG-CRG/TonsilAtlas
Glossary	This paper	Data S1 and https://doi.org/10.6084/m9.figshare.24885063
Other
Scenic TF Database	Van de Sande et al.24	https://github.com/aertslab/SCENICprotocol/blob/master/example/allTFs_hg38.txt
CisTarget databases Hg38__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather motifs-v9-nr.hgnc-m0.001-o0.0.tbl	Herrmann et al.122 and Imrichová et al.123	https://resources.aertslab.org/cistarget/
JASPAR2020 v0.99.10	Fornes et al.124 and Tan and Lenhard125	https://bioconductor.org/packages/release/data/annotation/html/JASPAR2020.html
chromVARmotifs v0.2.0	Schep et al.111	https://github.com/GreenleafLab/chromVARmotifs
Deposited data
Fastq files	This paper	ArrayExpress: E-MTAB-13687
Outputs CellRanger (expression and accessibility matrices)	This paper	https://doi.org/10.5281/zenodo.10373041
Seurat objects	This paper	https://doi.org/10.5281/zenodo.8373756