REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
D1H2	Cell Signaling	Cat# 4499; RRID:AB_10544537
C36B11	Cell Signaling	Cat# 9733; RRID:AB_2616029
EP1601Y	Abcam	Cat# ab214586; RRID:AB_869890
10/Fibronectin	BD Biosciences	Cat# 610078; RRID:AB_397486
TAL 1B5	Abcam	Cat# ab20181; RRID:AB_445401
C51	Cell Signaling	Cat# 4546; RRID:AB_2134843
HI98	Biolegend	Cat# 301902; RRID:AB_314194
KP1	Thermo Fisher	Cat# 14-0688-82; RRID:AB_11151139
polyclonal_PA5-16722	Thermo Fischer	Cat# PA5-16722; RRID:AB_10980222
1A4	Abcam	Cat# 7817; RRID:AB_262054
D21H3	Cell Signaling	Cat# 5741; RRID:AB_10695459
9E10	Biolegend	Cat# 626802; RRID:AB_2148451
3B5	BD Biosciences	Cat# 554299; RRID:AB_395352
polyclonal_A0452	Dako	Cat# A0542; RRID:AB_2335677
HTA28	Biolegend	Cat# 641002; RRID:AB_1227659
EP1347Y	Abcam	Cat# ab216655; RRID:AB_2864379
100	Biolegend	Cat# 658702; RRID:AB_2562959
EP1	Epitomics	Cat# IR084
EPR4097	Abcam	Cat# ab108398; RRID:AB_10863604
SP1	Abcam	Cat# ab187260; RRID:AB_2927684
EP2	Epitomics	Cat# AC-0028EU
SP2	Abcam	Cat# ab239793; RRID:AB_2927687
7F5	Cell Signaling	Cat# 2527; RRID:AB_10695803
polyclonal_CD44	R&D Systems	Cat# AF3660; RRID:AB_10971655
D6F11	Cell Signaling	Cat# 5153; RRID:AB_10691711
UCHL1	Biolegend	Cat# 304202; RRID:AB_314418
HI100	Biolegend	Cat# 304120; RRID:AB_493763
2B11	Thermo Fisher	Cat# 14-9457-82; RRID:AB_11063696
L50-823	BD Biosciences	Cat# 558686; RRID:AB_2108590
L26	Thermo Fisher	Cat# 14-0202-82; RRID:AB_10734340
C8/144B	Thermo Fisher	Cat# 14-0085-82; RRID:AB_11150240
polyclonal_CA9_AF2188	R&D Systems	Cat# AF2188; RRID:AB_416562
36/E-Cadherin	BD Biosciences	Cat# 610182; RRID:AB_397581
B56	BD Biosciences	Cat# 556003; RRID:AB_396287
D38B1	Cell Signaling	Cat# 4267; RRID:AB_2246311
D57.2.2E	Cell Signaling	Cat# 4858; RRID:AB_916156
Polyclonal_CD4_AF-379	R&D Systems	Cat# AF-379; RRID:AB_354469
poly vwf	Millipore	Cat# AB7356; RRID:AB_92216
EPR3094	Abcam	Cat# ab207090; RRID:AB_2889382
49F9	Cell Signaling	Cat# 2976; RRID:AB_490932
RCK105	Abcam	Cat# ab9021; RRID:AB_306947
AE3	Millipore	Cat# MAB1611; RRID:AB_2134409
AE1	Millipore	Cat# MAB1612; RRID:AB_2132794
C92-605	BD Biosciences	Cat# 559565; RRID:AB_397274
F21-852	BD Biosciences	Cat# 552596; RRID:AB_394437
Biological samples
ZTMA 21 (TMA containing mostly primary tumor cores)	University Hospital Zurich	Ethics: BASEC-PB-2019-1111 Table S1
ZTMA 25 (TMA containing mostly lymph node metastasis cores)	University Hospital Zurich	Ethics: BASEC-PB-2019-1111 Table S1
ZTMA 26 (TMA containing mostly primary tumor cores)	University Hospital Zurich	Ethics: BASEC-PB-2019-111 Table S1
Deposited data
IMC raw data of ZTMA 21 and 25	Zenodo	Zenodo: https://doi.org/10.5281/zenodo.7494413
IMC raw data of ZTMA 26, all TMAs’ extracted single-cell data and associated metadata (incl. patient data), IF images and extracted single-cell data of whole primary breast cancer sections	Zenodo	Zenodo: https://doi.org/10.5281/zenodo.7494509
IMC image stacks and single-cell masks in tiff format, Scans and extracted single-cell data of IHC stains on ZTMA 25	Zenodo	Zenodo: https://doi.org/10.5281/zenodo.7494727
Software and algorithms
Processing and analysis code for this study	GitHub and Zenodo	Github: https://github.com/BodenmillerGroup/BC_LN_metastses; Zenodo: https://doi.org/10.5281/zenodo.7650864
IMC preprocessing pipeline	GitHub	Github: https://github.com/BodenmillerGroup/ImcSegmentationPipeline