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. 2024 Apr 12;5(5):101511. doi: 10.1016/j.xcrm.2024.101511
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Anti-huCD56 BV605, Clone HCD56 (mouse IgG1k) BioLegend Cat#318334; RRID: AB_2561912
Chemicals, peptides, and recombinant proteins
4′,6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) Invitrogen Cat#D1306
Dimethyl sulfoxide (DMSO) Sigma Aldrich Cat#D2650
Dulbecco′s 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 Cat#11140050
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
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-tumour-microenvironment-0
Original source dataset of primary TNBC tumors Wu et al.12 https://singlecell.broadinstitute.org/single_cell/study/SCP1106/stromal-cell-diversity-associated-with-immune-evasion-in-human-triple-negative-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-invasive-carcinoma-ffpe-1-standard-1-3-0; https://www.10xgenomics.com/datasets/human-breast-cancer-visium-fresh-frozen-whole-transcriptome-1-standard; https://www.10xgenomics.com/datasets/human-breast-cancer-block-a-section-1-1-standard-1-1-0; https://www.10xgenomics.com/datasets/human-breast-cancer-whole-transcriptome-analysis-1-standard-1-2-0; https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast
I-SPY2-990 mRNA and clinical data for I-SPY2 trial Nanda et al.57 GEO: GSE194040