KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Brilliant Violet 605™ Anti-Human CD19 Antibody | BioLegend | Cat# 363023, RRID:AB_2564252; Cat# 363035, RRID:AB_2632786 |
| APC-H7 Mouse Anti-Human CD20 | BD Biosciences | Cat# 641396, RRID:AB_1645724 |
| LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit | Thermofisher | Cat# L34965 |
| 7-AAD Viability Staining | BioLegend | Cat# 420404 |
| Biological samples | ||
| Fresh or frozen surgical biopsies of DLBCL, FL and tonsil samples | This paper | N/A |
| Critical commercial assays | ||
| clonoSEQ® | https://www.clonoseq.com/ | N/A |
| Chromium Single Cell 5’ Library & Gel Bead Kit, 16 rxns | 10x Genomics, Pleasanton, CA | Prod# 1000006 |
| Chromium Single Cell 5’ Library Construction Kit, 16 rxns | 10x Genomics, Pleasanton, CA | Prod# 1000020 |
| Chromium Single Cell V(D)J Enrichment Kit, Human B Cell, 96 rxns | 10x Genomics, Pleasanton, CA | Prod# 1000016 |
| Chromium Single Cell A Chip Kit, 48 rxn | 10x Genomics, Pleasanton, CA | Prod# 1000152 |
| Chromium i7 Multiplex Kit | 10x Genomics, Pleasanton, CA | Prod# 120262 |
| Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1, 16 rxns | 10x Genomics, Pleasanton, CA | Prod# 1000165 |
| Chromium Next GEM Chip G Single Cell Kit, 48 rxns | 10x Genomics, Pleasanton, CA | Prod# 1000120 |
| Single Index Kit T Set A, 96 rxns | 10x Genomics, Pleasanton, CA | Prod# 1000213 |
| Deposited data | ||
| DLBCL, FL and tonsil scRNA-seq | This paper | GEO: GSE182436 |
| Lymphoma and reactive lymph node samples scRNA-seq | Roider et al. (2020) | https://heidata.uni-heidelberg.de/dataset.xhtml?persistentId=doi:10.11588/data/VRJUNV |
| FL scRNA-seq | Andor et al. (2019) | Correspondence with authors |
| FL scRNA-seq | Zhang et al. (2019) | https://zenodo.org/record/3594331#.X42xh5Mzbxg |
| Reactive lymph node samples scRNA-seq | Aoki et al. (2020) | EGA: EGAS00001004085 |
| Tonsil samples scRNA-seq | King et al. (2021) | ArrayExpress: E-MTAB-8999 |
| DLBCL bulk-tissue RNA-seq | Schmitz et al. (2018) | https://gdc.cancer.gov/about-data/publications/DLBCL-2018 |
| DLBCL bulk-tissue RNA-seq | Ennishi et al. (2019) | EGA: EGAD00001003783 |
| DLBCL bulk-tissue RNA-seq | Reddy et al. (2017) | EGA: EGAD00001003600 |
| DLBCL bulk-tissue microarray | Chapuy et al. (2018) | GEO: GSE98588 |
| Bulk FL microarray samples | Newman et al. (2019) | GEO: GSE127472 |
| DLBCL microarray samples from the REMoDLB trial | Sha et al. (2019) | GEO: GSE117556 |
| Human lymph node Visium dataset (Space Ranger 1.0.0) | 10x Genomics | https://support.10xgenomics.com/spatial-gene-expression/datasets/1.0.0/V1_Human_Lymph_Node |
| Human reference genome NCBI build 38, GRCh38 | Genome Reference Consortium | http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/ |
| BrainArray (v23) | Dai et al. (2005) | http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp#v23 |
| LM22 signature matrix (CIBERSORTx) | Newman et al. (2015) | N/A |
| TR4 signature matrix (CIBERSORTx) | Newman et al. (2019) | N/A |
| Software and algorithms | ||
| EcoTyper (v1.0) | This work |
https://ecotyper.stanford.edu/
https://doi.org/10.25936/rssb-t744 |
| CIBERSORTx (v1.0) | Newman et al. (2019) | https://cibersortx.stanford.edu/ |
| 10x Genomics Cell Ranger (v2.1, v3.0 and v5.0) | Zheng et al. (2017) | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest |
| 10x Genomics Loupe V(D)J Browser (v3.0.0 and v4.0.0) | 10x Genomics website | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest |
| 10x Genomics Loupe Browser (v4.2.0.0) | 10x Genomics website | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest |
| CellPhoneDB (v2.1.1) | Efremova et al. (2020) | https://github.com/Teichlab/cellphonedb |
| Seurat R package (v2.3.4 and v3.1.3) | Butler et al. (2018); Stuart et al. (2019) | https://cran.r-project.org/web/packages/Seurat/index.html |
| CytoTRACE R package (v0.3.3) | Gulati et al. (2020) | https://cytotrace.stanford.edu/ |
| inferCNV R package (v1.5.0) | Tickle et al. (2019) | http://www.bioconductor.org/packages/release/bioc/html/infercnv.html |
| copynumber R package (v1.12.0) | Nilsen et al. (2012) | https://www.bioconductor.org/packages/release/bioc/html/copynumber.html |
| escape R package (v1.1.1) | Borcherding (2021) | https://bioconductor.org/packages/release/bioc/html/escape.html |
| FNN R package (v1.1.3) | Beygelzimer et al. (2021) | https://CRAN.R-project.org/package=FNN |
| MASS R package (v7.3–53.1) | Venables and Ripley (2002) | https://cran.r-project.org/web/packages/MASS/index.html |
| survival R package (v2.42.3) | Therneau and Grambsch (2000) | https://cran.r-project.org/web/packages/survival/index.html |
| fgsea R package (v1.8.0) | Korotkevich et al. (2021) | https://bioconductor.org/packages/release/bioc/html/fgsea.html |
| metap R package (v1.4) | Dewey (2020) | https://CRAN.R-project.org/package=metap |
| igraph R package (v1.2.2) | Csardi and Nepusz (2006) | https://CRAN.R-project.org/package=igraph |
| umap R package (v.0.2.0.0) | McInnes et al. (2018) | https://cran.r-project.org/web/packages/umap/index.html |
| Other | ||
| ToppFun website | Chen et al. (2009) | https://toppgene.cchmc.org/ |