KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| FITC-EpCAM | Stem Cell Technologies | 60136FI |
| APC-CD49f | BioLegend | 313616 |
| Biotin-CD2 | BD Biosciences | 555325 |
| Biotin-CD3 | BD Biosciences | 55338 |
| Biotin-CD16 | BD Biosciences | 555405 |
| Biotin-CD64 | BD Biosciences | 555526 |
| Biotin-CD31 | Invitrogen | MHCD31154 |
| Biotin-CD45 | BioLegend | 304004 |
| p63 | Cell Signaling Technology | 13109 |
| KRT7 | Abcam | AB68459 |
| KRT23 | Abcam | AB156569 |
| ER | Fisher Scientific | RM9101S |
| PR | Cell Signaling Technology | 8757 |
| TCF7 | Cell Signaling Technology | 2203 |
| P4HA1 | Thermo Fisher | PA5-55353 |
| LRRC26 | Thermo Fisher | PA5-63285 |
| Biological samples | ||
| Human breast specimens from reduction mammoplasty surgeries | CHTN and Kaiser Permanente Northern California | Table S1 |
| Human breast specimens from core biopsies | Komen Tissue Bank | Table S1 |
| Chemicals, peptides, and recombinant proteins | ||
| BV785-Streptavidin | BioLegend | 405249 |
| Collagenase Type 3 | Worthington | CLS-3 |
| Collagenase Type 2 | Worthington | CLS-2 |
| Hyaluronidase | Sigma Aldrich | H3506 |
| RPMI with HEPES | Corning | 10-041-CV |
| Amphotericin B | Lonza | 17-836E |
| Gentamicin | Lonza | 17-518 |
| Dispase | Stem Cell Technologies | 07913 |
| DNase I | Stem Cell Technologies | 07900 |
| MEGM | Lonza | CC-3150 |
| MEBM | Lonza | CC-3151 |
| Lab Vision Ultra-V Block | Thermo Fisher | TA-125-UB |
| UltraVision LP Detection System | Thermo Fisher | TL-060-HL |
| Vectashield HardSet Mounting Media with DAPI | Vector Labs | H-1400 |
| FITC-TSA | Akoya Biosciences | NEL701A001KT |
| Cy3-TSA | Akoya Biosciences | NEL744001KT |
| Cy5-TSA | Akoya Biosciences | NEL745E001KT |
| Probe Hs-ESR1 | ACD Bio | 310301 |
| Critical commercial assays | ||
| Chromium Single Cell 3’ Library & Gel Bead Kit v2 | 10X Genomics | PN-120237 |
| Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 | 10X Genomics | PN-1000075 |
| Chromium Single Cell A Chip Kit | 10X Genomics | PN-120236 |
| Chromium Single Cell B Chip Kit | 10X Genomics | PN-1000153 |
| Chromium i7 Multiplex Kit | 10X Genomics | PN-120262 |
| MULTI-seq Lipid-Modified Oligos | Millipore Sigma | LMO001-100RXN |
| Bioanalyzer High Sensitivity DNA Kit | Agilent | 5067-4626 |
| Qubit dsDNA HS Assay Kit | Thermo Fisher | Q32851 |
| RNAscope Multiplex Fluorescent Reagent Kit V2 | ACD Bio | 323100 |
| Deposited data | ||
| Raw data and processed scRNA-seq UMI counts and barcode matrices of reduction mammoplasty breast specimens | This study | GEO: GSE198732 |
| Raw data and processed scRNA-seq UMI counts and barcode matrices of Komen Tissue Bank breast specimens | This study | GEO: GSE198732 |
| Software and algorithms | ||
| CellRanger v3.0.2 | 10x Genomics | Github: https://github.com/10XGenomics/cellranger |
| MULTI-seq | McGinnis et al., 2019b | Github: https://github.com/chris-mcginnis-ucsf/MULTI-seq |
| SoupOrCell | Heaton et al., 2020 | Github: https://github.com/wheaton5/souporcell |
| Seurat v3.1.5 | Stuart et al., 2019; Hafemeister and Satija, 2019 | Github: https://github.com/satijalab/seurat |
| DoubletFinder | McGinnis et al., 2019a | Github: https://github.com/chris-mcginnis-ucsf/DoubletFinder |
| LIGER | Gao et al., 2021; Welch et al., 2019 | Github: https://github.com/welch-lab/liger |
| DECIPHER-seq computational workflow | This study | Github: https://github.com/lmurrow/DECIPHER-seq and https://doi.org/10.5281/zenodo.6596414 |
| ape | Desper and Gascuel, 2002 | Github: https://github.com/emmanuelparadis/ape |
| Leidenalg | Traag et al., 2011 | Github: https://github.com/vtraag/leidenalg |
| wTO | Gysi et al., 2018 | Github: https://github.com/cran/wTO |
| fgsea | Korotkevich et al., 2019 | Github: https://github.com/ctlab/fgsea |
| DESeq2 | Love et al., 2014 | Github: https://github.com/mikelove/DESeq2 |