| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rat anti-KRT8 (clone TROMA-1) | Sigma-Aldrich | Cat#MABT329; RRID:AB_2891089 |
| Rabbit anti-PLIN1 (polyclonal) | Thermo-Fisher Scientific | Cat#PA5-81240; RRID:AB_2788467 |
| Mouse anti-TCF4 (clone 6H5-3) | Sigma-Aldrich | Cat#05-511; RRID:AB_309772 |
| Mouse anti-Nur77 AF488 (clone 12.14) | Thermo-Fisher Scientific | Cat#53-5965-82; RRID:AB_2574429 |
| Mouse anti-INSR (clone MM0414-2A12) | Abcam | Cat#ab90940; RRID:AB_2127106 |
| Rabbit anti-CD45 (clone EP322Y) | Abcam | Cat#ab40763; RRID:AB_726545 |
| Mouse anti-CD68 (clone KP1) | Thermo-Fisher Scientific | Cat#MA5-13324; RRID:AB_10987212 |
| Rabbit anti-CD3e AF488 (clone EP449E) | Abcam | Cat#ab271850 |
| Goat anti-rabbit IgG AF488 | Thermo-Fisher Scientific | Cat#A11008; RRID:AB_143165 |
| Goat anti-rabbit IgG AF568 | Thermo-Fisher Scientific | Cat#A11011; RRID:AB_143157 |
| Donkey anti-mouse IgG AF568 | Thermo-Fisher Scientific | Cat#A10037; RRID:AB_2534013 |
| Goat anti-rat IgG Cy5 | Thermo-Fisher Scientific | Cat#A10525; RRID:AB_2534034 |
| See Table S3 for details on antibodies used for CODEX | N/A | N/A |
| Biological samples | ||
| Healthy breast tissue from female-to-male gender-affirmation surgeries and cis-gender cosmetic mammary surgeries | Cedars-Sinai Biobank and Research Pathology Resource | www.cedars-sinai.edu/research/cores/biobank-research-pathology.html |
| Chemicals, peptides, and recombinant proteins | ||
| Nuclei EZ Lysis Buffer | Sigma-Aldrich | Cat#NUC101-1KT |
| RiboLock RNase Inhibitor (40 U/μL) | Thermo-Fisher Scientific | Cat#EO0381 |
| Nonidet P40 Substitute | Sigma-Aldrich | Cat#11754599001 |
| Digitonin (5%) | Thermo-Fisher Scientific | Cat#BN2006 |
| BSA, Molecular Biology Grade | New England Biolabs | Cat#B9200 |
| Critical commercial assays | ||
| Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 | 10X Genomics | PN-1000075 |
| Chromium Single Cell B Chip Kit | 10X Genomics | PN-1000073 |
| Chromium i7 Multiplex Kit | 10X Genomics | PN-120262 |
| Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 | 10X Genomics | PN-1000175 |
| Chromium Next GEM Chip H Single Cell Kit | 10X Genomics | PN-1000161 |
| Single Index Kit N, Set A | 10X Genomics | PN-1000212 |
| 10X Buffer for CODEX | Akoya | Cat#7000001 |
| Assay Reagent for CODEX | Akoya | Cat#7000002 |
| Staining Kit for CODEX | Akoya | Cat#7000008 |
| Antibody Conjugation Kit | Akoya | Cat#7000009 |
| Nuclear Stain for CODEX | Akoya | Cat#7000003 |
| Deposited data | ||
| Raw and analyzed scRNA-seq and scATAC-seq data | This paper | GSE168838 |
| Processed imaging (CODEX) data | This paper | zenodo.6569916 |
| MSigDB; v7.2 | Subramanian & Tamayo et al.,123 Liberzon et al.,124 Liberzon et al.125 | www.gsea-msigdb.org/gsea/msigdb |
| Geno-type-Tissue Expression Project (GTEx); v8 | GTEx Consortium126 | gtexportal.org/home |
| Cis-BP: Catalog of Inferred Sequence Binding Preferences | Weirauch et al.127 | cisbp.ccbr.utoronto.ca |
| Software and algorithms | ||
| Cell Ranger; v6.0.1 | 10x Genomics | support.10xgenomics.com/single-cell-gene-expression/software |
| CellRanger ATAC; v1.2.0 | 10X Genomics | support.10xgenomics.com/single-cell-atac/software |
| Seurat; v4.1.0 | Hao & Hao et al.128 | satijalab.org/seurat |
| scVelo; v0.2.3 | Bergen et al.129 | scvelo.readthedocs.io |
| CellRank; v1.3 | Lange et al.130 | cellrank.readthedocs.io/en/stable |
| scDblFinder; v1.6.0 | Germain et al.131 | github.com/plger/scDblFinder |
| Harmony; v0.1.0 | Korsunsky et al.132 | github.com/immunogenomics/harmony |
| UMAP; v0.5 | McInnes et at.133 | github.com/lmcinnes/umap |
| Augur; v1.0.3 | Skinnider & Squair et al.134 | github.com/neurorestore/Augur |
| MAST; 1.21.3 | Finak et al.135 | rglab.github.io/MAST |
| SCANPY; v1.4.5.1 | Wolf et al.136 | scanpy.readthedocs.io/en/stable |
| g:Profiler; v0.2.1 | Raudvere et al.137 | biit.cs.ut.ee/gprofiler/gost |
| GRNboost2 | Moerman et al.138 | github.com/aertslab/GRNBoost |
| pySCENIC; v0.11.2 | Aibar et al.139 | scenic.aertslab.org |
| DESeq2; v1.32.0 | Love et al.140 | github.com/mikelove/DESeq2 |
| velocyto; v0.17.17 | La Manno et al.16 | http://velocyto.org |
| destiny; v3.0.1 | Angerer et al.141 | github.com/theislab/destiny |
| AICSImageIO; v3.3.7 | AICSImageIO Contributors142 | github.com/AllenCellModeling/aicsimageio |
| StarDist; v0.8.1 | Schmidt et al.143 and Weigert et al.144 | github.com/stardist/stardist |
| Rdist; v0.0.5 | The Comprehensive R Archive Network (CRAN) | github.com/blasern/rdist |
| APCluster; v1.4.9 | Frey & Dueck145 | github.com/UBod/apcluster |
| scikit-image; v0.19.1 | Van der Walt et al.146 | github.com/scikit-image/scikit-image |
| ArchR; v1.0.0 | Granja et al.147 | archrproject.com |
| chromVAR; v1.16.0 | Schep et al.148 | github.com/GreenleafLab/chromVAR |
| MACS2; v2.2.7.1 | Zhang et al.149 | github.com/macs3-project/MACS |
| randomForest; v4.6-14 | The Comprehensive R Archive Network (CRAN) | stat.berkeley.edu/∼breiman/RandomForests |
| Other | ||
| KIMBLE Dounce tissue grinder set | Sigma-Aldrich | Cat#D9063 |
| MACS SmartStrainers (70 μm) | Miltenyi | Cat#130-110-916 |
| Pre-Separation Filters (20 μm) | Miltenyi | Cat#130-101-812 |
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