other:
Article Title: Multi-level inhibition of coronavirus replication by chemical ER stress
Article Snippet: MRC-5 human embryonic lung fibroblasts (ATCC, CCL-171) were maintained in DMEM containing 1.5 g/l (w/v) NaHCO 3 and complemented with 10% fetal calf serum (FCS; PAN Biotech Cat No. 1502-P110704), 2 mM L-glutamine, 100 U/ml penicillin, and 100 μg/ml streptomycin, 1% minimum essential medium non-essential amino acids (100x MEM NEAA; Gibco Cat No 11140-035) and 1 mM sodium pyruvate (100 mM; Gibco 11360-039).
Article Title: PD-L1 ( CD274 ) promoter hypomethylation predicts immunotherapy response in metastatic urothelial carcinoma
Article Snippet: S 0615HI, Bio&SELL GmbH, Nuremberg, Germany), 1X MEM (Minimum Essential Medium) Non-Essential Amino Acids Solution (100X stock, cat. no. 11140035, Thermo Fisher Scientific), 1 mM sodium pyruvate (100 mM stock, cat. no. 11360070, Thermo Fisher Scientific), and 100 U/ml penicillin and streptomycin (10,000 U/ml stock, cat. no. 15140122, Thermo Fisher Scientific).
Article Title: CTLA4 DNA methylation is associated with CTLA-4 expression and predicts response to immunotherapy in head and neck squamous cell carcinoma
Article Snippet: S 0615HI, Bio&SELL GmbH, Nuremburg, Germany), 1X MEM (Minimum Essential Medium) Non-Essential Amino Acids Solution (100X stock, cat. no. 11140035, Thermo Fisher Scientific), 1 mM 2-mercaptoethanol (cat. no. 21985023, Thermo Fisher Scientific), 100 U/ml penicillin and streptomycin (10,000 U/ml stock, cat. no. 15140122, Thermo Fisher Scientific), and 1 mM sodium pyruvate (100 mM stock, cat. no. 11360070, Thermo Fisher Scientific).
Article Title: Preclinical pharmacokinetic characterization of amdizalisib, a novel PI3Kδ inhibitor for the treatment of hematological malignancies
Article Snippet: Fetal bovine serum (FBS), 1X high-glucose Dulbecco’s Modified Eagle Medium (DMEM), 0.05% (1X) trypsin–EDTA solution, 1X Hank’s balanced salt solution (HBSS), 1 M (100X) N-2-hydroxyethylpiperazine-N′-2-ethanesulfonic acid (HEPES), 100X penicillin–streptomycin solution, 100 mM (100X) sodium pyruvate, 200 mM (100X) L-glutamine, and 100X minimum essential medium-non-essential amino acid (MEM-NEAA) solution were obtained from Gibco (Invitrogen, Carlsbad, CA, United States).
Article Title: DNA methylation regulates TIGIT expression within the melanoma microenvironment, is prognostic for overall survival, and predicts progression-free survival in patients treated with anti-PD-1 immunotherapy.
Article Snippet: S 0615HI, Bio&SELL GmbH, Nuremburg, Germany), 1X MEM (Minimum Essential Medium) Non-Essential Amino Acids Solution (100X stock, cat. no. 11140035, Thermo Fisher Scientific), 1 mM HEPES (1 M stock, cat. no. 15630056, Thermo Fisher Scientific), 1 mM 2-mercaptoethanol (cat. no. 21985023, Thermo Fisher Scientific), 100 U/ml penicillin and streptomycin (10,000 U/ml stock, cat. no. 15140122, Thermo Fisher Scientific), and 1 mM sodium pyruvate (100 mM stock, cat. no. 11360070, Thermo Fisher Scientific).
Multiple Displacement Amplification:Article Title: MCT4 and CD147 co-localize with MMP14 in invadopodia and autolysosomes and collectively stimulate breast cancer cell invasion by increasing extracellular matrix degradation
Article Snippet: .. MDA-MB-231 cells were cultured in Dulbecco’s modified eagle medium (DMEM) 1885 (Substrat og SterilCentralen, #15, University of Copenhagen, Panum 13.01.111) supplemented with 10% Fetal Bovine Serum (FBS, Gibco, #F9665), 1% Penicillin/Streptomycin (Pen/Strep, Sigma-Aldrich, #P0781) and 1% minimum essential medium (MEM) Non-Essential Amino Acids 100x (NEAA, Gibco, #11140-035). .. For MDA-MB-231 with stable shRNA-mediated MCT4 KD (described in ( )) the media was supplemented with 1 μg/ml puromycin (Gibco, #A11138-02).
Article Title: A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-huCD56 BV605, Clone HCD56 (mouse IgG1k) BioLegend Cat#318334; RRID: AB_2561912 Chemicals, peptides, and recombinant proteins 40,6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) Invitrogen Cat#D1306 Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#D2650 Dulbecco0s Phosphate Buffered Saline (DPBS) Sigma Aldrich Cat#D8537 Fetal Bovine Serum (FBS) Corning Cat#35-011-CV Human IL-2 IS, premium grade Miltenyi Biotec Cat#130-097-746 RPMI-1640 Corning Cat#10-040-CV Penicillin-Streptomycin (100X) Cytiva HyClone Cat#SV30010 Sodium Pyruvate (100 mM) Gibco Cat#11360070 Minimum Essential Media (MEM) non-essential amino acids (NEAA) (100X) Gibco Cat11140050 GlutaMAX Supplement Gibco Cat#35050061 2-mercaptoethanol (50 mM) Gibco Cat#21985023 Critical commercial assays UltraComp eBeads Plus Compensation Beads Invitrogen Cat#01-3333-42 Deposited data Primary breast tumor atlas This paper https://doi.org/10.5281/zenodo.10672250 Experimental models: Cell lines NK-92 ATCC Cat#CRL-2407, RRID: CVCL_2142 BT-474 ATCC Cat#HTB-20, RRID: CVCL_0179 MDA-MB-436 ATCC Cat#HTB-130, RRID: CVCL_0623 K-562 ATCC Cat#CCL-243, RRID: CVCL_0004 Software and algorithms limma (v3.50.1) Ritchie et al.90 https://bioconductor.org/packages/release/ bioc/html/limma.html org.Hs.e.g.,.db (v3.14.0) Carlson et al.91 https://bioconductor.org/packages/release/ data/annotation/html/org.Hs.eg.db.html DoubletFinder (v2.0.3) McGinnis et al.92 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.1.0) Hao et al.93 https://satijalab.org/seurat/ MAST (v1.20.0) Finak et al.94 https://www.bioconductor.org/packages/ release/bioc/html/MAST.html SCTransform (v0.3.2.9008) Hafemeister et al.95 https://github.com/satijalab/sctransform UCell (v1.99.1) Andreatta et al.96 https://github.com/carmonalab/UCell clusterProfiler (v4.2.2) Wu et al.97 https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html msigdbr (v7.5.1) Dolgalev et al.98 https://cran.r-project.org/web/packages/ msigdbr/vignettes/msigdbr-intro.html TCGAbiolinks (v2.18.0) Colaprico et al.99 https://bioconductor.org/packages/release/ bioc/html/TCGAbiolinks.html DESeq2 (v1.34.0) Love et al.100 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html inferCNV (v.0.99.7) Tickle et al.101 https://github.com/broadinstitute/infercnv ROGUE Liu et al.52 https://github.com/PaulingLiu/ROGUE (Continued on next page) e1 Cell Reports Medicine 5, 101511, May 21, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER cola (v2.0.0) Gu et al.102 https://www.bioconductor.org/packages/ release/bioc/html/cola.html NicheNet (v1.1.0) Browaeys et al.103 https://github.com/saeyslab/nichenetr CellChat (v0.0.1) Jin et al.104 https://github.com/jinworks/CellChat BisqueRNA (v1.0.5) Jew et al.105 https://github.com/cozygene/bisque pROC (v1.18.0) Robin et al.106 https://cran.r-project.org/web/packages/ pROC/index.html Other Resource website for the primary breast tumor atlas publication containing dataset and analyses This paper https://github.com/ChanLab-UTSW/ BreastCancer_Integrated Original source dataset of immune cells in primary breast tumors Azizi et al.7 GEO: GSE114727 Original source dataset of primary TNBC tumors Karaayvaz et al.8 GEO: GSE118389 Original source dataset of primary breast tumors Pal et al.9 GEO: GSE161529 Original source dataset of T cells in primary TNBC tumors Savas et al.107 GEO: GSE110686 Original source dataset of primary breast tumors Wu et al.13 GEO: GSE176078 Original source dataset with primary breast tumors Xu et al.14 GEO: GSE180286 Original source dataset with primary breast tumors Qian et al.11 https://lambrechtslab.sites.vib.be/en/ pan-cancer-blueprint-tumourmicroenvironment-0 Original source dataset of primary TNBC tumors Wu et al.12 https://singlecell.broadinstitute.org/ single_cell/study/SCP1106/stromalcell-diversity-associated-withimmune-evasion-in-human-triplenegative-breast-cancer Original source dataset of PD-1 treated primary breast tumors Bassez et al.108 https://lambrechtslab.sites.vib. be/en/single-cell Breast cancer cell line data from DepMap 22Q2 public release Ghandi et al.109 https://depmap.org/portal/download/all/ Spatially resolved data for 6 primary breast tumors Wu et al.12 https://doi.org/10.5281/zenodo.4739739 Spatially resolved data from 5 primary breast tumors 10x Genomics https://www.10xgenomics.com/datasets/human- breast-cancer-ductal-carcinoma-in-situ-invasivecarcinoma-ffpe-1-standard-1-3-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-visium-fresh-frozen-wholetranscriptome-1-standard; https://www.10xgenomics.com/datasets/humanbreast-cancer-block-a-section-1-1-standard-1-1-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-whole-transcriptome-analysis-1standard-1-2-0; https://www.10xgenomics.com/products/xeniumin-situ/preview-dataset-human-breast I-SPY2-990 mRNA and clinical data for I-SPY2 trial Nanda et al.57 GEO: GSE194040 OPEN ACCESS
Cell Culture:Article Title: MCT4 and CD147 co-localize with MMP14 in invadopodia and autolysosomes and collectively stimulate breast cancer cell invasion by increasing extracellular matrix degradation
Article Snippet: .. MDA-MB-231 cells were cultured in Dulbecco’s modified eagle medium (DMEM) 1885 (Substrat og SterilCentralen, #15, University of Copenhagen, Panum 13.01.111) supplemented with 10% Fetal Bovine Serum (FBS, Gibco, #F9665), 1% Penicillin/Streptomycin (Pen/Strep, Sigma-Aldrich, #P0781) and 1% minimum essential medium (MEM) Non-Essential Amino Acids 100x (NEAA, Gibco, #11140-035). .. For MDA-MB-231 with stable shRNA-mediated MCT4 KD (described in ( )) the media was supplemented with 1 μg/ml puromycin (Gibco, #A11138-02).
Modification:Article Title: MCT4 and CD147 co-localize with MMP14 in invadopodia and autolysosomes and collectively stimulate breast cancer cell invasion by increasing extracellular matrix degradation
Article Snippet: .. MDA-MB-231 cells were cultured in Dulbecco’s modified eagle medium (DMEM) 1885 (Substrat og SterilCentralen, #15, University of Copenhagen, Panum 13.01.111) supplemented with 10% Fetal Bovine Serum (FBS, Gibco, #F9665), 1% Penicillin/Streptomycin (Pen/Strep, Sigma-Aldrich, #P0781) and 1% minimum essential medium (MEM) Non-Essential Amino Acids 100x (NEAA, Gibco, #11140-035). .. For MDA-MB-231 with stable shRNA-mediated MCT4 KD (described in ( )) the media was supplemented with 1 μg/ml puromycin (Gibco, #A11138-02).
Recombinant:Article Title: A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-huCD56 BV605, Clone HCD56 (mouse IgG1k) BioLegend Cat#318334; RRID: AB_2561912 Chemicals, peptides, and recombinant proteins 40,6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) Invitrogen Cat#D1306 Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#D2650 Dulbecco0s Phosphate Buffered Saline (DPBS) Sigma Aldrich Cat#D8537 Fetal Bovine Serum (FBS) Corning Cat#35-011-CV Human IL-2 IS, premium grade Miltenyi Biotec Cat#130-097-746 RPMI-1640 Corning Cat#10-040-CV Penicillin-Streptomycin (100X) Cytiva HyClone Cat#SV30010 Sodium Pyruvate (100 mM) Gibco Cat#11360070 Minimum Essential Media (MEM) non-essential amino acids (NEAA) (100X) Gibco Cat11140050 GlutaMAX Supplement Gibco Cat#35050061 2-mercaptoethanol (50 mM) Gibco Cat#21985023 Critical commercial assays UltraComp eBeads Plus Compensation Beads Invitrogen Cat#01-3333-42 Deposited data Primary breast tumor atlas This paper https://doi.org/10.5281/zenodo.10672250 Experimental models: Cell lines NK-92 ATCC Cat#CRL-2407, RRID: CVCL_2142 BT-474 ATCC Cat#HTB-20, RRID: CVCL_0179 MDA-MB-436 ATCC Cat#HTB-130, RRID: CVCL_0623 K-562 ATCC Cat#CCL-243, RRID: CVCL_0004 Software and algorithms limma (v3.50.1) Ritchie et al.90 https://bioconductor.org/packages/release/ bioc/html/limma.html org.Hs.e.g.,.db (v3.14.0) Carlson et al.91 https://bioconductor.org/packages/release/ data/annotation/html/org.Hs.eg.db.html DoubletFinder (v2.0.3) McGinnis et al.92 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.1.0) Hao et al.93 https://satijalab.org/seurat/ MAST (v1.20.0) Finak et al.94 https://www.bioconductor.org/packages/ release/bioc/html/MAST.html SCTransform (v0.3.2.9008) Hafemeister et al.95 https://github.com/satijalab/sctransform UCell (v1.99.1) Andreatta et al.96 https://github.com/carmonalab/UCell clusterProfiler (v4.2.2) Wu et al.97 https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html msigdbr (v7.5.1) Dolgalev et al.98 https://cran.r-project.org/web/packages/ msigdbr/vignettes/msigdbr-intro.html TCGAbiolinks (v2.18.0) Colaprico et al.99 https://bioconductor.org/packages/release/ bioc/html/TCGAbiolinks.html DESeq2 (v1.34.0) Love et al.100 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html inferCNV (v.0.99.7) Tickle et al.101 https://github.com/broadinstitute/infercnv ROGUE Liu et al.52 https://github.com/PaulingLiu/ROGUE (Continued on next page) e1 Cell Reports Medicine 5, 101511, May 21, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER cola (v2.0.0) Gu et al.102 https://www.bioconductor.org/packages/ release/bioc/html/cola.html NicheNet (v1.1.0) Browaeys et al.103 https://github.com/saeyslab/nichenetr CellChat (v0.0.1) Jin et al.104 https://github.com/jinworks/CellChat BisqueRNA (v1.0.5) Jew et al.105 https://github.com/cozygene/bisque pROC (v1.18.0) Robin et al.106 https://cran.r-project.org/web/packages/ pROC/index.html Other Resource website for the primary breast tumor atlas publication containing dataset and analyses This paper https://github.com/ChanLab-UTSW/ BreastCancer_Integrated Original source dataset of immune cells in primary breast tumors Azizi et al.7 GEO: GSE114727 Original source dataset of primary TNBC tumors Karaayvaz et al.8 GEO: GSE118389 Original source dataset of primary breast tumors Pal et al.9 GEO: GSE161529 Original source dataset of T cells in primary TNBC tumors Savas et al.107 GEO: GSE110686 Original source dataset of primary breast tumors Wu et al.13 GEO: GSE176078 Original source dataset with primary breast tumors Xu et al.14 GEO: GSE180286 Original source dataset with primary breast tumors Qian et al.11 https://lambrechtslab.sites.vib.be/en/ pan-cancer-blueprint-tumourmicroenvironment-0 Original source dataset of primary TNBC tumors Wu et al.12 https://singlecell.broadinstitute.org/ single_cell/study/SCP1106/stromalcell-diversity-associated-withimmune-evasion-in-human-triplenegative-breast-cancer Original source dataset of PD-1 treated primary breast tumors Bassez et al.108 https://lambrechtslab.sites.vib. be/en/single-cell Breast cancer cell line data from DepMap 22Q2 public release Ghandi et al.109 https://depmap.org/portal/download/all/ Spatially resolved data for 6 primary breast tumors Wu et al.12 https://doi.org/10.5281/zenodo.4739739 Spatially resolved data from 5 primary breast tumors 10x Genomics https://www.10xgenomics.com/datasets/human- breast-cancer-ductal-carcinoma-in-situ-invasivecarcinoma-ffpe-1-standard-1-3-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-visium-fresh-frozen-wholetranscriptome-1-standard; https://www.10xgenomics.com/datasets/humanbreast-cancer-block-a-section-1-1-standard-1-1-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-whole-transcriptome-analysis-1standard-1-2-0; https://www.10xgenomics.com/products/xeniumin-situ/preview-dataset-human-breast I-SPY2-990 mRNA and clinical data for I-SPY2 trial Nanda et al.57 GEO: GSE194040 OPEN ACCESS
Saline:Article Title: A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-huCD56 BV605, Clone HCD56 (mouse IgG1k) BioLegend Cat#318334; RRID: AB_2561912 Chemicals, peptides, and recombinant proteins 40,6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) Invitrogen Cat#D1306 Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#D2650 Dulbecco0s Phosphate Buffered Saline (DPBS) Sigma Aldrich Cat#D8537 Fetal Bovine Serum (FBS) Corning Cat#35-011-CV Human IL-2 IS, premium grade Miltenyi Biotec Cat#130-097-746 RPMI-1640 Corning Cat#10-040-CV Penicillin-Streptomycin (100X) Cytiva HyClone Cat#SV30010 Sodium Pyruvate (100 mM) Gibco Cat#11360070 Minimum Essential Media (MEM) non-essential amino acids (NEAA) (100X) Gibco Cat11140050 GlutaMAX Supplement Gibco Cat#35050061 2-mercaptoethanol (50 mM) Gibco Cat#21985023 Critical commercial assays UltraComp eBeads Plus Compensation Beads Invitrogen Cat#01-3333-42 Deposited data Primary breast tumor atlas This paper https://doi.org/10.5281/zenodo.10672250 Experimental models: Cell lines NK-92 ATCC Cat#CRL-2407, RRID: CVCL_2142 BT-474 ATCC Cat#HTB-20, RRID: CVCL_0179 MDA-MB-436 ATCC Cat#HTB-130, RRID: CVCL_0623 K-562 ATCC Cat#CCL-243, RRID: CVCL_0004 Software and algorithms limma (v3.50.1) Ritchie et al.90 https://bioconductor.org/packages/release/ bioc/html/limma.html org.Hs.e.g.,.db (v3.14.0) Carlson et al.91 https://bioconductor.org/packages/release/ data/annotation/html/org.Hs.eg.db.html DoubletFinder (v2.0.3) McGinnis et al.92 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.1.0) Hao et al.93 https://satijalab.org/seurat/ MAST (v1.20.0) Finak et al.94 https://www.bioconductor.org/packages/ release/bioc/html/MAST.html SCTransform (v0.3.2.9008) Hafemeister et al.95 https://github.com/satijalab/sctransform UCell (v1.99.1) Andreatta et al.96 https://github.com/carmonalab/UCell clusterProfiler (v4.2.2) Wu et al.97 https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html msigdbr (v7.5.1) Dolgalev et al.98 https://cran.r-project.org/web/packages/ msigdbr/vignettes/msigdbr-intro.html TCGAbiolinks (v2.18.0) Colaprico et al.99 https://bioconductor.org/packages/release/ bioc/html/TCGAbiolinks.html DESeq2 (v1.34.0) Love et al.100 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html inferCNV (v.0.99.7) Tickle et al.101 https://github.com/broadinstitute/infercnv ROGUE Liu et al.52 https://github.com/PaulingLiu/ROGUE (Continued on next page) e1 Cell Reports Medicine 5, 101511, May 21, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER cola (v2.0.0) Gu et al.102 https://www.bioconductor.org/packages/ release/bioc/html/cola.html NicheNet (v1.1.0) Browaeys et al.103 https://github.com/saeyslab/nichenetr CellChat (v0.0.1) Jin et al.104 https://github.com/jinworks/CellChat BisqueRNA (v1.0.5) Jew et al.105 https://github.com/cozygene/bisque pROC (v1.18.0) Robin et al.106 https://cran.r-project.org/web/packages/ pROC/index.html Other Resource website for the primary breast tumor atlas publication containing dataset and analyses This paper https://github.com/ChanLab-UTSW/ BreastCancer_Integrated Original source dataset of immune cells in primary breast tumors Azizi et al.7 GEO: GSE114727 Original source dataset of primary TNBC tumors Karaayvaz et al.8 GEO: GSE118389 Original source dataset of primary breast tumors Pal et al.9 GEO: GSE161529 Original source dataset of T cells in primary TNBC tumors Savas et al.107 GEO: GSE110686 Original source dataset of primary breast tumors Wu et al.13 GEO: GSE176078 Original source dataset with primary breast tumors Xu et al.14 GEO: GSE180286 Original source dataset with primary breast tumors Qian et al.11 https://lambrechtslab.sites.vib.be/en/ pan-cancer-blueprint-tumourmicroenvironment-0 Original source dataset of primary TNBC tumors Wu et al.12 https://singlecell.broadinstitute.org/ single_cell/study/SCP1106/stromalcell-diversity-associated-withimmune-evasion-in-human-triplenegative-breast-cancer Original source dataset of PD-1 treated primary breast tumors Bassez et al.108 https://lambrechtslab.sites.vib. be/en/single-cell Breast cancer cell line data from DepMap 22Q2 public release Ghandi et al.109 https://depmap.org/portal/download/all/ Spatially resolved data for 6 primary breast tumors Wu et al.12 https://doi.org/10.5281/zenodo.4739739 Spatially resolved data from 5 primary breast tumors 10x Genomics https://www.10xgenomics.com/datasets/human- breast-cancer-ductal-carcinoma-in-situ-invasivecarcinoma-ffpe-1-standard-1-3-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-visium-fresh-frozen-wholetranscriptome-1-standard; https://www.10xgenomics.com/datasets/humanbreast-cancer-block-a-section-1-1-standard-1-1-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-whole-transcriptome-analysis-1standard-1-2-0; https://www.10xgenomics.com/products/xeniumin-situ/preview-dataset-human-breast I-SPY2-990 mRNA and clinical data for I-SPY2 trial Nanda et al.57 GEO: GSE194040 OPEN ACCESS
Software:Article Title: A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-huCD56 BV605, Clone HCD56 (mouse IgG1k) BioLegend Cat#318334; RRID: AB_2561912 Chemicals, peptides, and recombinant proteins 40,6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) Invitrogen Cat#D1306 Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#D2650 Dulbecco0s Phosphate Buffered Saline (DPBS) Sigma Aldrich Cat#D8537 Fetal Bovine Serum (FBS) Corning Cat#35-011-CV Human IL-2 IS, premium grade Miltenyi Biotec Cat#130-097-746 RPMI-1640 Corning Cat#10-040-CV Penicillin-Streptomycin (100X) Cytiva HyClone Cat#SV30010 Sodium Pyruvate (100 mM) Gibco Cat#11360070 Minimum Essential Media (MEM) non-essential amino acids (NEAA) (100X) Gibco Cat11140050 GlutaMAX Supplement Gibco Cat#35050061 2-mercaptoethanol (50 mM) Gibco Cat#21985023 Critical commercial assays UltraComp eBeads Plus Compensation Beads Invitrogen Cat#01-3333-42 Deposited data Primary breast tumor atlas This paper https://doi.org/10.5281/zenodo.10672250 Experimental models: Cell lines NK-92 ATCC Cat#CRL-2407, RRID: CVCL_2142 BT-474 ATCC Cat#HTB-20, RRID: CVCL_0179 MDA-MB-436 ATCC Cat#HTB-130, RRID: CVCL_0623 K-562 ATCC Cat#CCL-243, RRID: CVCL_0004 Software and algorithms limma (v3.50.1) Ritchie et al.90 https://bioconductor.org/packages/release/ bioc/html/limma.html org.Hs.e.g.,.db (v3.14.0) Carlson et al.91 https://bioconductor.org/packages/release/ data/annotation/html/org.Hs.eg.db.html DoubletFinder (v2.0.3) McGinnis et al.92 https://github.com/chris-mcginnis-ucsf/DoubletFinder Seurat (v4.1.0) Hao et al.93 https://satijalab.org/seurat/ MAST (v1.20.0) Finak et al.94 https://www.bioconductor.org/packages/ release/bioc/html/MAST.html SCTransform (v0.3.2.9008) Hafemeister et al.95 https://github.com/satijalab/sctransform UCell (v1.99.1) Andreatta et al.96 https://github.com/carmonalab/UCell clusterProfiler (v4.2.2) Wu et al.97 https://bioconductor.org/packages/release/ bioc/html/clusterProfiler.html msigdbr (v7.5.1) Dolgalev et al.98 https://cran.r-project.org/web/packages/ msigdbr/vignettes/msigdbr-intro.html TCGAbiolinks (v2.18.0) Colaprico et al.99 https://bioconductor.org/packages/release/ bioc/html/TCGAbiolinks.html DESeq2 (v1.34.0) Love et al.100 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html inferCNV (v.0.99.7) Tickle et al.101 https://github.com/broadinstitute/infercnv ROGUE Liu et al.52 https://github.com/PaulingLiu/ROGUE (Continued on next page) e1 Cell Reports Medicine 5, 101511, May 21, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER cola (v2.0.0) Gu et al.102 https://www.bioconductor.org/packages/ release/bioc/html/cola.html NicheNet (v1.1.0) Browaeys et al.103 https://github.com/saeyslab/nichenetr CellChat (v0.0.1) Jin et al.104 https://github.com/jinworks/CellChat BisqueRNA (v1.0.5) Jew et al.105 https://github.com/cozygene/bisque pROC (v1.18.0) Robin et al.106 https://cran.r-project.org/web/packages/ pROC/index.html Other Resource website for the primary breast tumor atlas publication containing dataset and analyses This paper https://github.com/ChanLab-UTSW/ BreastCancer_Integrated Original source dataset of immune cells in primary breast tumors Azizi et al.7 GEO: GSE114727 Original source dataset of primary TNBC tumors Karaayvaz et al.8 GEO: GSE118389 Original source dataset of primary breast tumors Pal et al.9 GEO: GSE161529 Original source dataset of T cells in primary TNBC tumors Savas et al.107 GEO: GSE110686 Original source dataset of primary breast tumors Wu et al.13 GEO: GSE176078 Original source dataset with primary breast tumors Xu et al.14 GEO: GSE180286 Original source dataset with primary breast tumors Qian et al.11 https://lambrechtslab.sites.vib.be/en/ pan-cancer-blueprint-tumourmicroenvironment-0 Original source dataset of primary TNBC tumors Wu et al.12 https://singlecell.broadinstitute.org/ single_cell/study/SCP1106/stromalcell-diversity-associated-withimmune-evasion-in-human-triplenegative-breast-cancer Original source dataset of PD-1 treated primary breast tumors Bassez et al.108 https://lambrechtslab.sites.vib. be/en/single-cell Breast cancer cell line data from DepMap 22Q2 public release Ghandi et al.109 https://depmap.org/portal/download/all/ Spatially resolved data for 6 primary breast tumors Wu et al.12 https://doi.org/10.5281/zenodo.4739739 Spatially resolved data from 5 primary breast tumors 10x Genomics https://www.10xgenomics.com/datasets/human- breast-cancer-ductal-carcinoma-in-situ-invasivecarcinoma-ffpe-1-standard-1-3-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-visium-fresh-frozen-wholetranscriptome-1-standard; https://www.10xgenomics.com/datasets/humanbreast-cancer-block-a-section-1-1-standard-1-1-0; https://www.10xgenomics.com/datasets/humanbreast-cancer-whole-transcriptome-analysis-1standard-1-2-0; https://www.10xgenomics.com/products/xeniumin-situ/preview-dataset-human-breast I-SPY2-990 mRNA and clinical data for I-SPY2 trial Nanda et al.57 GEO: GSE194040 OPEN ACCESS
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