Single Cell:Article Title: Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Fresh tissue samples Karolinska University Hospital See Table S1 for details Critical commercial assays Chromium Next GEM Single-Cell 5′ Kit v2 10× Genomics Cat#PN-1000263 Chromium Single Cell Human BCR Amplification Kit 10× Genomics Cat#PN-1000253 DNeasy Tissue and Blood Kit Qiagen Cat#69506 EasySep human B-cell enrichment kit STEMCELL Cat#19054 PANO 7-plex IHC kit Panovue Cat#0004100100 Antibodies Anti-CD70 [E3Q1A] Cell Signaling Technology Cat#CST69209 Anti-CD20 [EP459Y] Abcam Cat#ab78237; RRID:AB_1640323 Anti-CCND1 [SP4] Abcam Cat#ab16663; RRID:AB_443423 Anti-CD4 ZSGB-BIO Cat#ZM0418; RRID:AB_2890106 Anti-FOXP3 [BP6166] BioLynx Cat#BX50188 Anti-PD1[D4W2J] Cell Signaling Technology Cat#CST86163; RRID:AB_2728833 Anti-CD8A [C8/144B] Cell Signaling Technology Cat#CST70306; RRID:AB_2799781 Anti-CD27 [M-T271] BD Biosciences Cat#555439; RRID:AB_395832 Experimental models: Cell lines Human: JVM-2 ATCC CRL-3002; RRID:CVCL_1319 Deposited data Raw scRNA-seq and WGS data This paper https://doi.org/10.48723/kfy8-5r05 H5 files of processed scRNA-seq data This paper GEO: GSE303064 Somatic mutations file of processed WGS data This paper Zenodo Data: https://doi.org/10.5281/zenodo.16098829 Code for scRNA-seq analysis This paper Github: https://github.com/wanhui5867/MCL-scRNAseq/ Fastq files of scRNA-seq data of normal bone marrow samples EMBL-EBI EMBL-EBI: E-MTAB-11536 scRNAseq matrics of gene expression and cell annotation of reactive lymph node samples Han et al.38 https://cellxgene.cziscience.com/collections/ 968834a0-1895-40df-8720-666029b3bbac Software and algorithms QuPath 0.5.1 Bankhead et al.72 https://qupath.github.io/ Cell Ranger 7.0.0 10× Genomics https://www.10xgenomics.com/ support/software/cell-ranger/ Seurat 4.3.0 Satija Lab https://satijalab.org/seurat/ inferCNV 1.16.0 Broad Institute https://github.com/broadinstitute/infercnv Monocle 2.28.0 Trapnell Lab https://cole-trapnell-lab.github.io/ monocle-release/ LIANA 0.1.13 Saez Lab https://github.com/saezlab/liana/ R 4.3.0 R Core Team https://www.r-project.org/ SHazaM 1.1.2 Immcantation Portal https://shazam.readthedocs.io/ Djvdj 0.1.0 Sheridan R 2023 https://github.com/rnabioco/djvdj/ Fishplot 0.5.1 Miller et al.73 https://github.com/chrisamiller/fishplot/ CloneVol 0.99.11 Dang et al.50 https://github.com/hdng/clonevol/ ABSOLUTE Broad Institute http://broadinstitute.org/software/ABSOLUTE e1 Cell Reports Medicine 6, 102318, September 16, 2025 Article ll OPEN ACCESS ..
Article Title: Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Fresh tissue samples Karolinska University Hospital See Table S1 for details Critical commercial assays Chromium Next GEM Single-Cell 5 ′ Kit v2 10× Genomics Cat#PN-1000263 Chromium Single Cell Human BCR Amplification Kit 10× Genomics Cat#PN-1000253 DNeasy Tissue and Blood Kit Qiagen Cat#69506 EasySep human B-cell enrichment kit STEMCELL Cat#19054 PANO 7-plex IHC kit Panovue Cat#0004100100 Antibodies Anti-CD70 [E3Q1A] Cell Signaling Technology Cat#CST69209 Anti-CD20 [EP459Y] Abcam Cat#ab78237; RRID:AB_1640323 Anti-CCND1 [SP4] Abcam Cat#ab16663; RRID:AB_443423 Anti-CD4 ZSGB-BIO Cat#ZM0418; RRID:AB_2890106 Anti-FOXP3 [BP6166] BioLynx Cat#BX50188 Anti-PD1[D4W2J] Cell Signaling Technology Cat#CST86163; RRID:AB_2728833 Anti-CD8A [C8/144B] Cell Signaling Technology Cat#CST70306; RRID:AB_2799781 Anti-CD27 [M-T271] BD Biosciences Cat#555439; RRID:AB_395832 Experimental models: Cell lines Human: JVM-2 ATCC CRL-3002; RRID:CVCL_1319 Deposited data Raw scRNA-seq and WGS data This paper https://doi.org/10.48723/kfy8-5r05 H5 files of processed scRNA-seq data This paper GEO: GSE303064 Somatic mutations file of processed WGS data This paper Zenodo Data: https://doi.org/10.5281/zenodo.16098829 Code for scRNA-seq analysis This paper Github: https://github.com/wanhui5867/MCL-scRNAseq/ Fastq files of scRNA-seq data of normal bone marrow samples EMBL-EBI EMBL-EBI: E-MTAB-11536 scRNAseq matrics of gene expression and cell annotation of reactive lymph node samples Han et al. 38 https://cellxgene.cziscience.com/collections/ 968834a0-1895-40df-8720-666029b3bbac Software and algorithms QuPath 0.5.1 Bankhead et al. 72 https://qupath.github.io/ Cell Ranger 7.0.0 10× Genomics https://www.10xgenomics.com/ support/software/cell-ranger/ Seurat 4.3.0 Satija Lab https://satijalab.org/seurat/ inferCNV 1.16.0 Broad Institute https://github.com/broadinstitute/infercnv Monocle 2.28.0 Trapnell Lab https://cole-trapnell-lab.github.io/ monocle-release/ LIANA 0.1.13 Saez Lab https://github.com/saezlab/liana/ R 4.3.0 R Core Team https://www.r-project.org/ SHazaM 1.1.2 Immcantation Portal https://shazam.readthedocs.io/ Djvdj 0.1.0 Sheridan R 2023 https://github.com/rnabioco/djvdj/ Fishplot 0.5.1 Miller et al. 73 https://github.com/chrisamiller/fishplot/ CloneVol 0.99.11 Dang et al. 50 https://github.com/hdng/clonevol/ ABSOLUTE Broad Institute http://broadinstitute.org/software/ABSOLUTE e1 Cell Reports Medicine 6, 102318, September 16, 2025 OPEN ACCESS ..
Amplification:Article Title: Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Fresh tissue samples Karolinska University Hospital See Table S1 for details Critical commercial assays Chromium Next GEM Single-Cell 5′ Kit v2 10× Genomics Cat#PN-1000263 Chromium Single Cell Human BCR Amplification Kit 10× Genomics Cat#PN-1000253 DNeasy Tissue and Blood Kit Qiagen Cat#69506 EasySep human B-cell enrichment kit STEMCELL Cat#19054 PANO 7-plex IHC kit Panovue Cat#0004100100 Antibodies Anti-CD70 [E3Q1A] Cell Signaling Technology Cat#CST69209 Anti-CD20 [EP459Y] Abcam Cat#ab78237; RRID:AB_1640323 Anti-CCND1 [SP4] Abcam Cat#ab16663; RRID:AB_443423 Anti-CD4 ZSGB-BIO Cat#ZM0418; RRID:AB_2890106 Anti-FOXP3 [BP6166] BioLynx Cat#BX50188 Anti-PD1[D4W2J] Cell Signaling Technology Cat#CST86163; RRID:AB_2728833 Anti-CD8A [C8/144B] Cell Signaling Technology Cat#CST70306; RRID:AB_2799781 Anti-CD27 [M-T271] BD Biosciences Cat#555439; RRID:AB_395832 Experimental models: Cell lines Human: JVM-2 ATCC CRL-3002; RRID:CVCL_1319 Deposited data Raw scRNA-seq and WGS data This paper https://doi.org/10.48723/kfy8-5r05 H5 files of processed scRNA-seq data This paper GEO: GSE303064 Somatic mutations file of processed WGS data This paper Zenodo Data: https://doi.org/10.5281/zenodo.16098829 Code for scRNA-seq analysis This paper Github: https://github.com/wanhui5867/MCL-scRNAseq/ Fastq files of scRNA-seq data of normal bone marrow samples EMBL-EBI EMBL-EBI: E-MTAB-11536 scRNAseq matrics of gene expression and cell annotation of reactive lymph node samples Han et al.38 https://cellxgene.cziscience.com/collections/ 968834a0-1895-40df-8720-666029b3bbac Software and algorithms QuPath 0.5.1 Bankhead et al.72 https://qupath.github.io/ Cell Ranger 7.0.0 10× Genomics https://www.10xgenomics.com/ support/software/cell-ranger/ Seurat 4.3.0 Satija Lab https://satijalab.org/seurat/ inferCNV 1.16.0 Broad Institute https://github.com/broadinstitute/infercnv Monocle 2.28.0 Trapnell Lab https://cole-trapnell-lab.github.io/ monocle-release/ LIANA 0.1.13 Saez Lab https://github.com/saezlab/liana/ R 4.3.0 R Core Team https://www.r-project.org/ SHazaM 1.1.2 Immcantation Portal https://shazam.readthedocs.io/ Djvdj 0.1.0 Sheridan R 2023 https://github.com/rnabioco/djvdj/ Fishplot 0.5.1 Miller et al.73 https://github.com/chrisamiller/fishplot/ CloneVol 0.99.11 Dang et al.50 https://github.com/hdng/clonevol/ ABSOLUTE Broad Institute http://broadinstitute.org/software/ABSOLUTE e1 Cell Reports Medicine 6, 102318, September 16, 2025 Article ll OPEN ACCESS ..
Article Title: Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Fresh tissue samples Karolinska University Hospital See Table S1 for details Critical commercial assays Chromium Next GEM Single-Cell 5 ′ Kit v2 10× Genomics Cat#PN-1000263 Chromium Single Cell Human BCR Amplification Kit 10× Genomics Cat#PN-1000253 DNeasy Tissue and Blood Kit Qiagen Cat#69506 EasySep human B-cell enrichment kit STEMCELL Cat#19054 PANO 7-plex IHC kit Panovue Cat#0004100100 Antibodies Anti-CD70 [E3Q1A] Cell Signaling Technology Cat#CST69209 Anti-CD20 [EP459Y] Abcam Cat#ab78237; RRID:AB_1640323 Anti-CCND1 [SP4] Abcam Cat#ab16663; RRID:AB_443423 Anti-CD4 ZSGB-BIO Cat#ZM0418; RRID:AB_2890106 Anti-FOXP3 [BP6166] BioLynx Cat#BX50188 Anti-PD1[D4W2J] Cell Signaling Technology Cat#CST86163; RRID:AB_2728833 Anti-CD8A [C8/144B] Cell Signaling Technology Cat#CST70306; RRID:AB_2799781 Anti-CD27 [M-T271] BD Biosciences Cat#555439; RRID:AB_395832 Experimental models: Cell lines Human: JVM-2 ATCC CRL-3002; RRID:CVCL_1319 Deposited data Raw scRNA-seq and WGS data This paper https://doi.org/10.48723/kfy8-5r05 H5 files of processed scRNA-seq data This paper GEO: GSE303064 Somatic mutations file of processed WGS data This paper Zenodo Data: https://doi.org/10.5281/zenodo.16098829 Code for scRNA-seq analysis This paper Github: https://github.com/wanhui5867/MCL-scRNAseq/ Fastq files of scRNA-seq data of normal bone marrow samples EMBL-EBI EMBL-EBI: E-MTAB-11536 scRNAseq matrics of gene expression and cell annotation of reactive lymph node samples Han et al. 38 https://cellxgene.cziscience.com/collections/ 968834a0-1895-40df-8720-666029b3bbac Software and algorithms QuPath 0.5.1 Bankhead et al. 72 https://qupath.github.io/ Cell Ranger 7.0.0 10× Genomics https://www.10xgenomics.com/ support/software/cell-ranger/ Seurat 4.3.0 Satija Lab https://satijalab.org/seurat/ inferCNV 1.16.0 Broad Institute https://github.com/broadinstitute/infercnv Monocle 2.28.0 Trapnell Lab https://cole-trapnell-lab.github.io/ monocle-release/ LIANA 0.1.13 Saez Lab https://github.com/saezlab/liana/ R 4.3.0 R Core Team https://www.r-project.org/ SHazaM 1.1.2 Immcantation Portal https://shazam.readthedocs.io/ Djvdj 0.1.0 Sheridan R 2023 https://github.com/rnabioco/djvdj/ Fishplot 0.5.1 Miller et al. 73 https://github.com/chrisamiller/fishplot/ CloneVol 0.99.11 Dang et al. 50 https://github.com/hdng/clonevol/ ABSOLUTE Broad Institute http://broadinstitute.org/software/ABSOLUTE e1 Cell Reports Medicine 6, 102318, September 16, 2025 OPEN ACCESS ..
Immunohistochemistry:Article Title: Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Fresh tissue samples Karolinska University Hospital See Table S1 for details Critical commercial assays Chromium Next GEM Single-Cell 5′ Kit v2 10× Genomics Cat#PN-1000263 Chromium Single Cell Human BCR Amplification Kit 10× Genomics Cat#PN-1000253 DNeasy Tissue and Blood Kit Qiagen Cat#69506 EasySep human B-cell enrichment kit STEMCELL Cat#19054 PANO 7-plex IHC kit Panovue Cat#0004100100 Antibodies Anti-CD70 [E3Q1A] Cell Signaling Technology Cat#CST69209 Anti-CD20 [EP459Y] Abcam Cat#ab78237; RRID:AB_1640323 Anti-CCND1 [SP4] Abcam Cat#ab16663; RRID:AB_443423 Anti-CD4 ZSGB-BIO Cat#ZM0418; RRID:AB_2890106 Anti-FOXP3 [BP6166] BioLynx Cat#BX50188 Anti-PD1[D4W2J] Cell Signaling Technology Cat#CST86163; RRID:AB_2728833 Anti-CD8A [C8/144B] Cell Signaling Technology Cat#CST70306; RRID:AB_2799781 Anti-CD27 [M-T271] BD Biosciences Cat#555439; RRID:AB_395832 Experimental models: Cell lines Human: JVM-2 ATCC CRL-3002; RRID:CVCL_1319 Deposited data Raw scRNA-seq and WGS data This paper https://doi.org/10.48723/kfy8-5r05 H5 files of processed scRNA-seq data This paper GEO: GSE303064 Somatic mutations file of processed WGS data This paper Zenodo Data: https://doi.org/10.5281/zenodo.16098829 Code for scRNA-seq analysis This paper Github: https://github.com/wanhui5867/MCL-scRNAseq/ Fastq files of scRNA-seq data of normal bone marrow samples EMBL-EBI EMBL-EBI: E-MTAB-11536 scRNAseq matrics of gene expression and cell annotation of reactive lymph node samples Han et al.38 https://cellxgene.cziscience.com/collections/ 968834a0-1895-40df-8720-666029b3bbac Software and algorithms QuPath 0.5.1 Bankhead et al.72 https://qupath.github.io/ Cell Ranger 7.0.0 10× Genomics https://www.10xgenomics.com/ support/software/cell-ranger/ Seurat 4.3.0 Satija Lab https://satijalab.org/seurat/ inferCNV 1.16.0 Broad Institute https://github.com/broadinstitute/infercnv Monocle 2.28.0 Trapnell Lab https://cole-trapnell-lab.github.io/ monocle-release/ LIANA 0.1.13 Saez Lab https://github.com/saezlab/liana/ R 4.3.0 R Core Team https://www.r-project.org/ SHazaM 1.1.2 Immcantation Portal https://shazam.readthedocs.io/ Djvdj 0.1.0 Sheridan R 2023 https://github.com/rnabioco/djvdj/ Fishplot 0.5.1 Miller et al.73 https://github.com/chrisamiller/fishplot/ CloneVol 0.99.11 Dang et al.50 https://github.com/hdng/clonevol/ ABSOLUTE Broad Institute http://broadinstitute.org/software/ABSOLUTE e1 Cell Reports Medicine 6, 102318, September 16, 2025 Article ll OPEN ACCESS ..
Article Title: Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Fresh tissue samples Karolinska University Hospital See Table S1 for details Critical commercial assays Chromium Next GEM Single-Cell 5 ′ Kit v2 10× Genomics Cat#PN-1000263 Chromium Single Cell Human BCR Amplification Kit 10× Genomics Cat#PN-1000253 DNeasy Tissue and Blood Kit Qiagen Cat#69506 EasySep human B-cell enrichment kit STEMCELL Cat#19054 PANO 7-plex IHC kit Panovue Cat#0004100100 Antibodies Anti-CD70 [E3Q1A] Cell Signaling Technology Cat#CST69209 Anti-CD20 [EP459Y] Abcam Cat#ab78237; RRID:AB_1640323 Anti-CCND1 [SP4] Abcam Cat#ab16663; RRID:AB_443423 Anti-CD4 ZSGB-BIO Cat#ZM0418; RRID:AB_2890106 Anti-FOXP3 [BP6166] BioLynx Cat#BX50188 Anti-PD1[D4W2J] Cell Signaling Technology Cat#CST86163; RRID:AB_2728833 Anti-CD8A [C8/144B] Cell Signaling Technology Cat#CST70306; RRID:AB_2799781 Anti-CD27 [M-T271] BD Biosciences Cat#555439; RRID:AB_395832 Experimental models: Cell lines Human: JVM-2 ATCC CRL-3002; RRID:CVCL_1319 Deposited data Raw scRNA-seq and WGS data This paper https://doi.org/10.48723/kfy8-5r05 H5 files of processed scRNA-seq data This paper GEO: GSE303064 Somatic mutations file of processed WGS data This paper Zenodo Data: https://doi.org/10.5281/zenodo.16098829 Code for scRNA-seq analysis This paper Github: https://github.com/wanhui5867/MCL-scRNAseq/ Fastq files of scRNA-seq data of normal bone marrow samples EMBL-EBI EMBL-EBI: E-MTAB-11536 scRNAseq matrics of gene expression and cell annotation of reactive lymph node samples Han et al. 38 https://cellxgene.cziscience.com/collections/ 968834a0-1895-40df-8720-666029b3bbac Software and algorithms QuPath 0.5.1 Bankhead et al. 72 https://qupath.github.io/ Cell Ranger 7.0.0 10× Genomics https://www.10xgenomics.com/ support/software/cell-ranger/ Seurat 4.3.0 Satija Lab https://satijalab.org/seurat/ inferCNV 1.16.0 Broad Institute https://github.com/broadinstitute/infercnv Monocle 2.28.0 Trapnell Lab https://cole-trapnell-lab.github.io/ monocle-release/ LIANA 0.1.13 Saez Lab https://github.com/saezlab/liana/ R 4.3.0 R Core Team https://www.r-project.org/ SHazaM 1.1.2 Immcantation Portal https://shazam.readthedocs.io/ Djvdj 0.1.0 Sheridan R 2023 https://github.com/rnabioco/djvdj/ Fishplot 0.5.1 Miller et al. 73 https://github.com/chrisamiller/fishplot/ CloneVol 0.99.11 Dang et al. 50 https://github.com/hdng/clonevol/ ABSOLUTE Broad Institute http://broadinstitute.org/software/ABSOLUTE e1 Cell Reports Medicine 6, 102318, September 16, 2025 OPEN ACCESS ..
Whole Complete genome sequencing:Article Title: Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Fresh tissue samples Karolinska University Hospital See Table S1 for details Critical commercial assays Chromium Next GEM Single-Cell 5′ Kit v2 10× Genomics Cat#PN-1000263 Chromium Single Cell Human BCR Amplification Kit 10× Genomics Cat#PN-1000253 DNeasy Tissue and Blood Kit Qiagen Cat#69506 EasySep human B-cell enrichment kit STEMCELL Cat#19054 PANO 7-plex IHC kit Panovue Cat#0004100100 Antibodies Anti-CD70 [E3Q1A] Cell Signaling Technology Cat#CST69209 Anti-CD20 [EP459Y] Abcam Cat#ab78237; RRID:AB_1640323 Anti-CCND1 [SP4] Abcam Cat#ab16663; RRID:AB_443423 Anti-CD4 ZSGB-BIO Cat#ZM0418; RRID:AB_2890106 Anti-FOXP3 [BP6166] BioLynx Cat#BX50188 Anti-PD1[D4W2J] Cell Signaling Technology Cat#CST86163; RRID:AB_2728833 Anti-CD8A [C8/144B] Cell Signaling Technology Cat#CST70306; RRID:AB_2799781 Anti-CD27 [M-T271] BD Biosciences Cat#555439; RRID:AB_395832 Experimental models: Cell lines Human: JVM-2 ATCC CRL-3002; RRID:CVCL_1319 Deposited data Raw scRNA-seq and WGS data This paper https://doi.org/10.48723/kfy8-5r05 H5 files of processed scRNA-seq data This paper GEO: GSE303064 Somatic mutations file of processed WGS data This paper Zenodo Data: https://doi.org/10.5281/zenodo.16098829 Code for scRNA-seq analysis This paper Github: https://github.com/wanhui5867/MCL-scRNAseq/ Fastq files of scRNA-seq data of normal bone marrow samples EMBL-EBI EMBL-EBI: E-MTAB-11536 scRNAseq matrics of gene expression and cell annotation of reactive lymph node samples Han et al.38 https://cellxgene.cziscience.com/collections/ 968834a0-1895-40df-8720-666029b3bbac Software and algorithms QuPath 0.5.1 Bankhead et al.72 https://qupath.github.io/ Cell Ranger 7.0.0 10× Genomics https://www.10xgenomics.com/ support/software/cell-ranger/ Seurat 4.3.0 Satija Lab https://satijalab.org/seurat/ inferCNV 1.16.0 Broad Institute https://github.com/broadinstitute/infercnv Monocle 2.28.0 Trapnell Lab https://cole-trapnell-lab.github.io/ monocle-release/ LIANA 0.1.13 Saez Lab https://github.com/saezlab/liana/ R 4.3.0 R Core Team https://www.r-project.org/ SHazaM 1.1.2 Immcantation Portal https://shazam.readthedocs.io/ Djvdj 0.1.0 Sheridan R 2023 https://github.com/rnabioco/djvdj/ Fishplot 0.5.1 Miller et al.73 https://github.com/chrisamiller/fishplot/ CloneVol 0.99.11 Dang et al.50 https://github.com/hdng/clonevol/ ABSOLUTE Broad Institute http://broadinstitute.org/software/ABSOLUTE e1 Cell Reports Medicine 6, 102318, September 16, 2025 Article ll OPEN ACCESS ..
Article Title: Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Fresh tissue samples Karolinska University Hospital See Table S1 for details Critical commercial assays Chromium Next GEM Single-Cell 5 ′ Kit v2 10× Genomics Cat#PN-1000263 Chromium Single Cell Human BCR Amplification Kit 10× Genomics Cat#PN-1000253 DNeasy Tissue and Blood Kit Qiagen Cat#69506 EasySep human B-cell enrichment kit STEMCELL Cat#19054 PANO 7-plex IHC kit Panovue Cat#0004100100 Antibodies Anti-CD70 [E3Q1A] Cell Signaling Technology Cat#CST69209 Anti-CD20 [EP459Y] Abcam Cat#ab78237; RRID:AB_1640323 Anti-CCND1 [SP4] Abcam Cat#ab16663; RRID:AB_443423 Anti-CD4 ZSGB-BIO Cat#ZM0418; RRID:AB_2890106 Anti-FOXP3 [BP6166] BioLynx Cat#BX50188 Anti-PD1[D4W2J] Cell Signaling Technology Cat#CST86163; RRID:AB_2728833 Anti-CD8A [C8/144B] Cell Signaling Technology Cat#CST70306; RRID:AB_2799781 Anti-CD27 [M-T271] BD Biosciences Cat#555439; RRID:AB_395832 Experimental models: Cell lines Human: JVM-2 ATCC CRL-3002; RRID:CVCL_1319 Deposited data Raw scRNA-seq and WGS data This paper https://doi.org/10.48723/kfy8-5r05 H5 files of processed scRNA-seq data This paper GEO: GSE303064 Somatic mutations file of processed WGS data This paper Zenodo Data: https://doi.org/10.5281/zenodo.16098829 Code for scRNA-seq analysis This paper Github: https://github.com/wanhui5867/MCL-scRNAseq/ Fastq files of scRNA-seq data of normal bone marrow samples EMBL-EBI EMBL-EBI: E-MTAB-11536 scRNAseq matrics of gene expression and cell annotation of reactive lymph node samples Han et al. 38 https://cellxgene.cziscience.com/collections/ 968834a0-1895-40df-8720-666029b3bbac Software and algorithms QuPath 0.5.1 Bankhead et al. 72 https://qupath.github.io/ Cell Ranger 7.0.0 10× Genomics https://www.10xgenomics.com/ support/software/cell-ranger/ Seurat 4.3.0 Satija Lab https://satijalab.org/seurat/ inferCNV 1.16.0 Broad Institute https://github.com/broadinstitute/infercnv Monocle 2.28.0 Trapnell Lab https://cole-trapnell-lab.github.io/ monocle-release/ LIANA 0.1.13 Saez Lab https://github.com/saezlab/liana/ R 4.3.0 R Core Team https://www.r-project.org/ SHazaM 1.1.2 Immcantation Portal https://shazam.readthedocs.io/ Djvdj 0.1.0 Sheridan R 2023 https://github.com/rnabioco/djvdj/ Fishplot 0.5.1 Miller et al. 73 https://github.com/chrisamiller/fishplot/ CloneVol 0.99.11 Dang et al. 50 https://github.com/hdng/clonevol/ ABSOLUTE Broad Institute http://broadinstitute.org/software/ABSOLUTE e1 Cell Reports Medicine 6, 102318, September 16, 2025 OPEN ACCESS ..
Gene Expression:Article Title: Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Fresh tissue samples Karolinska University Hospital See Table S1 for details Critical commercial assays Chromium Next GEM Single-Cell 5′ Kit v2 10× Genomics Cat#PN-1000263 Chromium Single Cell Human BCR Amplification Kit 10× Genomics Cat#PN-1000253 DNeasy Tissue and Blood Kit Qiagen Cat#69506 EasySep human B-cell enrichment kit STEMCELL Cat#19054 PANO 7-plex IHC kit Panovue Cat#0004100100 Antibodies Anti-CD70 [E3Q1A] Cell Signaling Technology Cat#CST69209 Anti-CD20 [EP459Y] Abcam Cat#ab78237; RRID:AB_1640323 Anti-CCND1 [SP4] Abcam Cat#ab16663; RRID:AB_443423 Anti-CD4 ZSGB-BIO Cat#ZM0418; RRID:AB_2890106 Anti-FOXP3 [BP6166] BioLynx Cat#BX50188 Anti-PD1[D4W2J] Cell Signaling Technology Cat#CST86163; RRID:AB_2728833 Anti-CD8A [C8/144B] Cell Signaling Technology Cat#CST70306; RRID:AB_2799781 Anti-CD27 [M-T271] BD Biosciences Cat#555439; RRID:AB_395832 Experimental models: Cell lines Human: JVM-2 ATCC CRL-3002; RRID:CVCL_1319 Deposited data Raw scRNA-seq and WGS data This paper https://doi.org/10.48723/kfy8-5r05 H5 files of processed scRNA-seq data This paper GEO: GSE303064 Somatic mutations file of processed WGS data This paper Zenodo Data: https://doi.org/10.5281/zenodo.16098829 Code for scRNA-seq analysis This paper Github: https://github.com/wanhui5867/MCL-scRNAseq/ Fastq files of scRNA-seq data of normal bone marrow samples EMBL-EBI EMBL-EBI: E-MTAB-11536 scRNAseq matrics of gene expression and cell annotation of reactive lymph node samples Han et al.38 https://cellxgene.cziscience.com/collections/ 968834a0-1895-40df-8720-666029b3bbac Software and algorithms QuPath 0.5.1 Bankhead et al.72 https://qupath.github.io/ Cell Ranger 7.0.0 10× Genomics https://www.10xgenomics.com/ support/software/cell-ranger/ Seurat 4.3.0 Satija Lab https://satijalab.org/seurat/ inferCNV 1.16.0 Broad Institute https://github.com/broadinstitute/infercnv Monocle 2.28.0 Trapnell Lab https://cole-trapnell-lab.github.io/ monocle-release/ LIANA 0.1.13 Saez Lab https://github.com/saezlab/liana/ R 4.3.0 R Core Team https://www.r-project.org/ SHazaM 1.1.2 Immcantation Portal https://shazam.readthedocs.io/ Djvdj 0.1.0 Sheridan R 2023 https://github.com/rnabioco/djvdj/ Fishplot 0.5.1 Miller et al.73 https://github.com/chrisamiller/fishplot/ CloneVol 0.99.11 Dang et al.50 https://github.com/hdng/clonevol/ ABSOLUTE Broad Institute http://broadinstitute.org/software/ABSOLUTE e1 Cell Reports Medicine 6, 102318, September 16, 2025 Article ll OPEN ACCESS ..
Article Title: Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Fresh tissue samples Karolinska University Hospital See Table S1 for details Critical commercial assays Chromium Next GEM Single-Cell 5 ′ Kit v2 10× Genomics Cat#PN-1000263 Chromium Single Cell Human BCR Amplification Kit 10× Genomics Cat#PN-1000253 DNeasy Tissue and Blood Kit Qiagen Cat#69506 EasySep human B-cell enrichment kit STEMCELL Cat#19054 PANO 7-plex IHC kit Panovue Cat#0004100100 Antibodies Anti-CD70 [E3Q1A] Cell Signaling Technology Cat#CST69209 Anti-CD20 [EP459Y] Abcam Cat#ab78237; RRID:AB_1640323 Anti-CCND1 [SP4] Abcam Cat#ab16663; RRID:AB_443423 Anti-CD4 ZSGB-BIO Cat#ZM0418; RRID:AB_2890106 Anti-FOXP3 [BP6166] BioLynx Cat#BX50188 Anti-PD1[D4W2J] Cell Signaling Technology Cat#CST86163; RRID:AB_2728833 Anti-CD8A [C8/144B] Cell Signaling Technology Cat#CST70306; RRID:AB_2799781 Anti-CD27 [M-T271] BD Biosciences Cat#555439; RRID:AB_395832 Experimental models: Cell lines Human: JVM-2 ATCC CRL-3002; RRID:CVCL_1319 Deposited data Raw scRNA-seq and WGS data This paper https://doi.org/10.48723/kfy8-5r05 H5 files of processed scRNA-seq data This paper GEO: GSE303064 Somatic mutations file of processed WGS data This paper Zenodo Data: https://doi.org/10.5281/zenodo.16098829 Code for scRNA-seq analysis This paper Github: https://github.com/wanhui5867/MCL-scRNAseq/ Fastq files of scRNA-seq data of normal bone marrow samples EMBL-EBI EMBL-EBI: E-MTAB-11536 scRNAseq matrics of gene expression and cell annotation of reactive lymph node samples Han et al. 38 https://cellxgene.cziscience.com/collections/ 968834a0-1895-40df-8720-666029b3bbac Software and algorithms QuPath 0.5.1 Bankhead et al. 72 https://qupath.github.io/ Cell Ranger 7.0.0 10× Genomics https://www.10xgenomics.com/ support/software/cell-ranger/ Seurat 4.3.0 Satija Lab https://satijalab.org/seurat/ inferCNV 1.16.0 Broad Institute https://github.com/broadinstitute/infercnv Monocle 2.28.0 Trapnell Lab https://cole-trapnell-lab.github.io/ monocle-release/ LIANA 0.1.13 Saez Lab https://github.com/saezlab/liana/ R 4.3.0 R Core Team https://www.r-project.org/ SHazaM 1.1.2 Immcantation Portal https://shazam.readthedocs.io/ Djvdj 0.1.0 Sheridan R 2023 https://github.com/rnabioco/djvdj/ Fishplot 0.5.1 Miller et al. 73 https://github.com/chrisamiller/fishplot/ CloneVol 0.99.11 Dang et al. 50 https://github.com/hdng/clonevol/ ABSOLUTE Broad Institute http://broadinstitute.org/software/ABSOLUTE e1 Cell Reports Medicine 6, 102318, September 16, 2025 OPEN ACCESS ..
Software:Article Title: Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Fresh tissue samples Karolinska University Hospital See Table S1 for details Critical commercial assays Chromium Next GEM Single-Cell 5′ Kit v2 10× Genomics Cat#PN-1000263 Chromium Single Cell Human BCR Amplification Kit 10× Genomics Cat#PN-1000253 DNeasy Tissue and Blood Kit Qiagen Cat#69506 EasySep human B-cell enrichment kit STEMCELL Cat#19054 PANO 7-plex IHC kit Panovue Cat#0004100100 Antibodies Anti-CD70 [E3Q1A] Cell Signaling Technology Cat#CST69209 Anti-CD20 [EP459Y] Abcam Cat#ab78237; RRID:AB_1640323 Anti-CCND1 [SP4] Abcam Cat#ab16663; RRID:AB_443423 Anti-CD4 ZSGB-BIO Cat#ZM0418; RRID:AB_2890106 Anti-FOXP3 [BP6166] BioLynx Cat#BX50188 Anti-PD1[D4W2J] Cell Signaling Technology Cat#CST86163; RRID:AB_2728833 Anti-CD8A [C8/144B] Cell Signaling Technology Cat#CST70306; RRID:AB_2799781 Anti-CD27 [M-T271] BD Biosciences Cat#555439; RRID:AB_395832 Experimental models: Cell lines Human: JVM-2 ATCC CRL-3002; RRID:CVCL_1319 Deposited data Raw scRNA-seq and WGS data This paper https://doi.org/10.48723/kfy8-5r05 H5 files of processed scRNA-seq data This paper GEO: GSE303064 Somatic mutations file of processed WGS data This paper Zenodo Data: https://doi.org/10.5281/zenodo.16098829 Code for scRNA-seq analysis This paper Github: https://github.com/wanhui5867/MCL-scRNAseq/ Fastq files of scRNA-seq data of normal bone marrow samples EMBL-EBI EMBL-EBI: E-MTAB-11536 scRNAseq matrics of gene expression and cell annotation of reactive lymph node samples Han et al.38 https://cellxgene.cziscience.com/collections/ 968834a0-1895-40df-8720-666029b3bbac Software and algorithms QuPath 0.5.1 Bankhead et al.72 https://qupath.github.io/ Cell Ranger 7.0.0 10× Genomics https://www.10xgenomics.com/ support/software/cell-ranger/ Seurat 4.3.0 Satija Lab https://satijalab.org/seurat/ inferCNV 1.16.0 Broad Institute https://github.com/broadinstitute/infercnv Monocle 2.28.0 Trapnell Lab https://cole-trapnell-lab.github.io/ monocle-release/ LIANA 0.1.13 Saez Lab https://github.com/saezlab/liana/ R 4.3.0 R Core Team https://www.r-project.org/ SHazaM 1.1.2 Immcantation Portal https://shazam.readthedocs.io/ Djvdj 0.1.0 Sheridan R 2023 https://github.com/rnabioco/djvdj/ Fishplot 0.5.1 Miller et al.73 https://github.com/chrisamiller/fishplot/ CloneVol 0.99.11 Dang et al.50 https://github.com/hdng/clonevol/ ABSOLUTE Broad Institute http://broadinstitute.org/software/ABSOLUTE e1 Cell Reports Medicine 6, 102318, September 16, 2025 Article ll OPEN ACCESS ..
Article Title: Tumor evolution and immune microenvironment dynamics in primary and relapsed mantle cell lymphoma.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Biological samples Fresh tissue samples Karolinska University Hospital See Table S1 for details Critical commercial assays Chromium Next GEM Single-Cell 5 ′ Kit v2 10× Genomics Cat#PN-1000263 Chromium Single Cell Human BCR Amplification Kit 10× Genomics Cat#PN-1000253 DNeasy Tissue and Blood Kit Qiagen Cat#69506 EasySep human B-cell enrichment kit STEMCELL Cat#19054 PANO 7-plex IHC kit Panovue Cat#0004100100 Antibodies Anti-CD70 [E3Q1A] Cell Signaling Technology Cat#CST69209 Anti-CD20 [EP459Y] Abcam Cat#ab78237; RRID:AB_1640323 Anti-CCND1 [SP4] Abcam Cat#ab16663; RRID:AB_443423 Anti-CD4 ZSGB-BIO Cat#ZM0418; RRID:AB_2890106 Anti-FOXP3 [BP6166] BioLynx Cat#BX50188 Anti-PD1[D4W2J] Cell Signaling Technology Cat#CST86163; RRID:AB_2728833 Anti-CD8A [C8/144B] Cell Signaling Technology Cat#CST70306; RRID:AB_2799781 Anti-CD27 [M-T271] BD Biosciences Cat#555439; RRID:AB_395832 Experimental models: Cell lines Human: JVM-2 ATCC CRL-3002; RRID:CVCL_1319 Deposited data Raw scRNA-seq and WGS data This paper https://doi.org/10.48723/kfy8-5r05 H5 files of processed scRNA-seq data This paper GEO: GSE303064 Somatic mutations file of processed WGS data This paper Zenodo Data: https://doi.org/10.5281/zenodo.16098829 Code for scRNA-seq analysis This paper Github: https://github.com/wanhui5867/MCL-scRNAseq/ Fastq files of scRNA-seq data of normal bone marrow samples EMBL-EBI EMBL-EBI: E-MTAB-11536 scRNAseq matrics of gene expression and cell annotation of reactive lymph node samples Han et al. 38 https://cellxgene.cziscience.com/collections/ 968834a0-1895-40df-8720-666029b3bbac Software and algorithms QuPath 0.5.1 Bankhead et al. 72 https://qupath.github.io/ Cell Ranger 7.0.0 10× Genomics https://www.10xgenomics.com/ support/software/cell-ranger/ Seurat 4.3.0 Satija Lab https://satijalab.org/seurat/ inferCNV 1.16.0 Broad Institute https://github.com/broadinstitute/infercnv Monocle 2.28.0 Trapnell Lab https://cole-trapnell-lab.github.io/ monocle-release/ LIANA 0.1.13 Saez Lab https://github.com/saezlab/liana/ R 4.3.0 R Core Team https://www.r-project.org/ SHazaM 1.1.2 Immcantation Portal https://shazam.readthedocs.io/ Djvdj 0.1.0 Sheridan R 2023 https://github.com/rnabioco/djvdj/ Fishplot 0.5.1 Miller et al. 73 https://github.com/chrisamiller/fishplot/ CloneVol 0.99.11 Dang et al. 50 https://github.com/hdng/clonevol/ ABSOLUTE Broad Institute http://broadinstitute.org/software/ABSOLUTE e1 Cell Reports Medicine 6, 102318, September 16, 2025 OPEN ACCESS ..
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