Antibodies |
|
Antibodies used for mass cytometry |
|
|
AKT (C67E7) - purified |
Cell Signaling Technologies |
Cat# 4691; RRID:AB_915783
|
Anti-rabbit IgG (polyclonal) - purified |
Vector Labs |
Cat# AI-1000; RRID:AB_2336193
|
AR (D6F11) - purified |
Cell Signaling Technologies |
Cat# 5153; RRID:AB_10692774
|
BCL-2 (100) - purified |
Biolegend |
Cat# 658702; RRID:AB_2562959
|
c-MET (D1C2) - purified |
Cell Signaling Technologies |
Cat# 8198; RRID:AB_10860590
|
c-MYC (D84C12) - purified |
Cell Signaling Technologies |
Cat# 5605; RRID:AB_1903938
|
CA9 (polyclonal) - purified |
R&D Systems |
Cat# AF2188; RRID:AB_416562
|
CD11b (M1/70) - purified |
Biolegend |
Cat# 101202; RRID:AB_312785
|
CD11c (Bu15) - purified |
Biolegend |
Cat# 337221; RRID:AB_2562834
|
CD123 (6H6) - purified |
Biolegend |
Cat# 306002; RRID:AB_314576
|
CD14 (RMO52) - purified |
Beckman Coulter |
Cat# A22331; RRID:AB_10639528
|
CD15 (HI98) - purified |
Biolegend |
Cat# 301902; RRID:AB_314194
|
CD16 (3G8) - purified |
Biolegend |
Cat# 302002; RRID:AB_314202
|
CD163 (GHI/61) - purified |
Biolegend |
Cat# 333602; RRID:AB_1088991
|
CD169 (7-239) - purified |
Biolegend |
Cat# 346002; RRID:AB_2189031
|
CD192/CCR2 (K036C2) - purified |
Biolegend |
Cat# 357202; RRID:AB_2561851
|
CD197/CCR7 (G043H7) - purified |
Biolegend |
Cat# 353202; RRID:AB_10945157
|
CD20 (H1(FB1)) - purified |
BD Biosciences |
Cat# 555677; RRID:AB_396030
|
CD204 (351615) - purified |
R&D Systems |
Cat# MAB2708; RRID:AB_2235696
|
CD206 (15-2) - purified |
Biolegend |
Cat# 321112; RRID:AB_571921
|
CD24 (ML5) - purified |
BD Biosciences |
Cat# 555426; RRID:AB_395820
|
CD25 (M-A251) - purified |
Biolegend |
Cat# 356102; RRID:AB_2561752
|
CD274/PD-L1 (E1L3N) - purified |
Cell Signaling Technologies |
Cat# 13684; RRID:AB_2687655
|
CD278/ICOS (C398.4A) - purified |
Biolegend |
Cat# 313502; RRID:AB_416326
|
CD279/PD-1 (EH12.2H7) - purified |
Biolegend |
Cat# 329902; RRID:AB_940488
|
CD3 (UCHT1) - purified |
Biolegend |
Cat# 300402; RRID:AB_314056
|
CD31 (HC1/6) - purified |
EMD Millipore |
Cat# CBL468-K; RRID:AB_1586934
|
CD32 (FUN-2) - purified |
Biolegend |
Cat# 303202; RRID:AB_314334
|
CD36 (5-271) - purified |
Biolegend |
Cat# 336215; RRID:AB_2563745
|
CD38 (HIT2) - purified |
Biolegend |
Cat# 303502; RRID:AB_314354
|
CD4 (RPA-T4) - purified |
Biolegend |
Cat# 300516; RRID:AB_314084
|
CD44 (IM7) - purified |
BD Biosciences |
Cat# 550538; RRID:AB_393732
|
CD45 (HI30) - purified |
Biolegend |
Cat# 304002; RRID:AB_314390
|
CD45RA (HI100) - purified |
Biolegend |
Cat# 304102; RRID:AB_314406
|
CD49f (GoH3) - purified |
Biolegend |
Cat# 313614; RRID:AB_893371
|
CD64 (10.1) - purified |
Biolegend |
Cat# 305002; RRID:AB_314486
|
CD68 (KP1) - purified |
Biolegend |
Cat# 916104; RRID:AB_2616797
|
CD68 (Y1/82A) - purified |
Biolegend |
Cat# 333802; RRID:AB_1089058
|
CD7 (M-T701) - purified |
BD Biosciences |
Cat# 555359; RRID:AB_395762
|
CD86 (233(FUN-1)) - purified |
BD Biosciences |
Cat# 555655; RRID:AB_396010
|
CD8a (RPA-T8) - purified |
Biolegend |
Cat# 301002; RRID:AB_314120
|
CD93 (R139) - purified |
eBioscience |
Cat# 14-0939-82; RRID:AB_891508
|
Cleaved CASPASE-3 (C92-605) - purified |
BD Biosciences |
Cat# 559565; RRID:AB_397274
|
Cleaved PARP-1 (F21-852) - purified |
BD Biosciences |
Cat# 552596; RRID:AB_394437
|
CTLA-4 (L3D10) - purified |
Biolegend |
Cat# 349902; RRID:AB_10642827
|
Cyclin B1 (GNS-11) - purified |
BD Biosciences |
Cat# 554179; RRID:AB_395290
|
E-CADHERIN (24E10) - purified |
Cell Signaling Technologies |
Cat# 3195; RRID:AB_10694492
|
E-CADHERIN (67A4) - purified |
Biolegend |
Cat# 324102; RRID:AB_756064
|
EGFR (EP38Y) - purified |
Abcam |
Cat# ab52894; RRID:AB_869579
|
EpCAM (9C4) - purified |
Biolegend |
Cat# 324202; RRID:AB_756076
|
ERα (EP1) - purified |
Epitomics |
Cat# AC-0015; RRID:AB_10704040
|
EZH2 (D2C9) - purified |
Cell Signaling Technologies |
Cat# 5246; RRID:AB_10694683
|
FAP (polyclonal) - purified |
R&D Systems |
Cat# AF3715; RRID:AB_2102369
|
FOXP3 (236A/E7) - purified |
ThermoFisher |
Cat# 14-4777-82; RRID:AB_467556
|
H3K27me3 (C36B11) - purified |
Cell Signaling Technologies |
Cat# 9733; RRID:AB_2616029
|
HER2 (3B5) - purified |
BD Biosciences |
Cat# 554299; RRID:AB_395352
|
HLA-DR (L243) - purified |
Biolegend |
Cat# 307602; RRID:AB_314680
|
K14 (polyclonal) - purified |
ThermoFisher |
Cat# PA5-16722; RRID:AB_10980222
|
K5 (EP1601Y) - purified |
Abcam |
Cat# ab52635; RRID:AB_869890
|
K7 (RCK105) - purified |
BD Biosciences |
Cat# 550507; RRID:AB_2134456
|
K8/18 (C51) - purified |
Cell Signaling Technologies |
Cat# 4546; RRID:AB_2134843
|
Ki-67 (8D5) - purified |
Cell Signaling Technologies |
Cat# 9449; RRID:AB_2715512
|
P53 (EPR17343) - purified |
Abcam |
Cat# ab179477; RRID:AB_2737134
|
Pan Keratin (AE1) - purified |
EMD Millipore |
Cat# MAB1612; RRID:AB_2132794
|
Pan Keratin (AE3) - purified |
EMD Millipore |
Cat# MAB1611; RRID:AB_2134409
|
PRB (YR85) - purified |
Abcam |
Cat# ab32085; RRID:AB_777452
|
PTEN (138G6) - purified |
Cell Signaling Technologies |
Cat# 9559; RRID:AB_390810
|
SLAMF7 (162.1) - purified |
Biolegend |
Cat# 331802; RRID:AB_961330
|
SMA (1A4) - purified |
Abcam |
Cat# ab8207; RRID:AB_306356
|
SURVIVIN (71G4B7) - purified |
Cell Signaling Technologies |
Cat# 2808; RRID:AB_10691694
|
TIM-3 (F38-2E2) - purified |
Biolegend |
Cat# 345035; RRID:AB_2566086
|
VIMENTIN (EPR3776) - purified |
Abcam |
Cat# ab92547; RRID:AB_10562134
|
|
Antibodies used for immunofluorescence |
|
CD3e (LN10) |
Leica |
Cat# NCL-L-CD3-565; RRID:AB_563541
|
CD68 (KP1) |
eBioscience/ThermoFisher |
Cat# 14-0688-82; RRID:AB_11151139
|
CTLA-4 (BSB-88) |
BIOSB |
Cat# BSB2884; RRID:AB_2762365
|
PD-1 (D4W2J) |
Cell Signaling Technologies |
Cat# 86163S; RRID:AB_2728833
|
PD-L1 (E1L3N) |
Cell Signaling Technologies |
Cat# 13684S; RRID:AB_2687655
|
Pan Keratin (h-240) |
Santa Cruz |
Cat# sc-15367; RRID:AB_2134438
|
EpCAM (EPR20532-225) |
Abcam |
Cat# ab223582; RRID:AB_2762366
|
Anti-mouse IgG (min X reactivity), HRP-conjugated (polyclonal) |
JacksonImmunoReseach |
Cat# 715-035-151; RRID:AB_2340771
|
Anti-rabbit IgG (min X reactivity), HRP-conjugated (polyclonal) |
JacksonImmunoReseach |
Cat# 711-035-152; RRID:AB_10015282
|
Anti-goat IgG (min X reactivity), HRP-conjugated (polyclonal) |
JacksonImmunoReseach |
Cat# 705-035-147; RRID:AB_2313587
|
|
Biological Samples |
|
Breast cancer and adjacent non-tumor tissue samples |
University Hospital Basel, University Hospital Zurich, Patient’s Tumor Bank of Hope (PATH), St. Johannes Hospital Dortmund and Institute of Pathology at Josefshaus, University Hospital Giessen and Marburg, Marburg site |
|
Reduction mammoplasty samples |
University Hospital Zurich |
|
Peripheral blood mononuclear cells (PBMCs) |
Zurich Blood Transfusion Service |
N/A |
|
Chemicals, Peptides, and Recombinant Proteins |
|
4′,6 diamidine-2-phenylindole (DAPI) |
ThermoFischer |
Cat# D1306 |
Antibody Stabilizer PBS |
Candor Bioscience |
Cat# 131 050 |
Bis(2,2′-bipyridine)-4′-methyl-4-carboxybipyridine-ruthenium-N-succidimyl ester-bis(hexafluorophosphate) (96Ru, 98-102Ru, 104Ru) |
Sigma Aldrich |
Cat# 96631 |
Bismuth trichloride (209Bi) |
Sigma Aldrich |
Cat# 450723 |
Bromoacetamidobenzyl-EDTA (BABE) |
Dojindo Laboratories |
Cat# B437-10 |
Cisplatin |
Fluidigm |
Cat# 201064 |
DMSO |
Sigma Aldrich |
Cat# D2438 |
EDTA |
StemCell Technologies, Inc. |
Cat# EDS-100G |
EQ™ Four Element Calibration Beads |
Fluidigm |
Cat# 201078 |
FcR Blocking Reagent, human |
Miltenyi Biotech |
Cat# 130-059-901 |
Indium (113In, 115In) |
Fluidigm |
N/A |
Iridium (191Ir, 193Ir) |
Fluidigm |
Cat# 201192A |
Lanthanide (III) metal isotopes as chloride salts |
Fluidigm |
N/A |
MACS Tissue Storage Solution |
Miltenyi Biotech |
Cat# 130-100-008 |
Magne Protein A Beads |
Promega |
Cat# G8781 |
Magne Protein G Beads |
Promega |
Cat# G7471 |
Maleimido-mono-amide-DOTA (mDOTA) |
Macrocyclics |
Cat# B-272 |
Palladium (105Pd, 106Pd, 108Pd, 110Pd) |
Fluidigm |
N/A |
Paraformaldehyde |
Electron Microscopy Sciences |
Cat# 15710 |
ProLong® Diamond Antifade Mountant |
Thermo Fisher |
Cat# P36961
|
Rhodium trichloride (103Rh) |
Sigma Aldrich |
Cat# 450286 |
Saponin |
Sigma Aldrich |
Cat# S7900 |
Trilogy 20x Concentrate |
CellMarque |
Cat# 920P-06 |
Yttrium (89Y) |
Sigma Aldrich |
N/A |
Critical Commercial Assays |
Opal 7-Color IHC Kit |
PerkinElmer |
Cat# NEL821001KT |
Tumor Dissociation Kit, human |
Miltenyi Biotech |
Cat# 130-095-929 |
Maxpar X8 Multimetal Labeling Kit |
Fluidigm |
Cat# 201300 |
|
Deposited Data |
|
Mass cytometry data |
This paper |
Mendeley Data https://doi.org/10.17632/gb83sywsjc.1
|
Immunofluorescence images |
This paper |
Mendeley Data https://doi.org/10.17632/gb83sywsjc.1
|
|
Experimental Models: Cell Lines |
|
MCF-10A |
American Type Culture Collection (ATCC) |
Cat# CRL-10317 |
MDA-MB-134-VI |
American Type Culture Collection (ATCC) |
Cat# HTB-23 |
MDA-MB-231 |
American Type Culture Collection (ATCC) |
Cat# HTB-26 |
MDA-MB-453 |
American Type Culture Collection (ATCC) |
Cat# HTB-131 |
SK-BR-3 |
American Type Culture Collection (ATCC) |
Cat# HTB-30 |
ZR-75-1 |
American Type Culture Collection (ATCC) |
Cat# CRL-1500 |
Fibroblasts |
Gift from the laboratory of Prof. Silvio Hemmi at the University of Zurich |
|
|
Software and Algorithms |
|
CATALYST |
Chevrier et al., 2018 |
http://bioconductor.org/packages/release/bioc/html/CATALYST.html |
circlize (R package) version 0.4.4 |
Gu et al., 2014 |
https://github.com/jokergoo/circlize |
Concatenation tool |
Cytobank, Inc |
https://support.cytobank.org/hc/en-us/articles/206336147-FCS-file-concatenation-tool |
Cytobank |
Kotecha et al., 2010 |
https://www.cytobank.org/ |
Fiji |
Schindelin et al., 2012 |
https://imagej.net/Welcome |
InForm Cell Analysis |
PerkinElmer |
http://www.perkinelmer.com |
MATLAB R2018a Neural Network Toolbox |
MathWorks, Inc., 2018 |
https://www.mathworks.com/ |
Normalizer |
Finck et al., 2013 |
https://github.com/nolanlab/bead-normalization/releases |
PhenoGraph |
Levine et al., 2015 |
https://github.com/jacoblevine/PhenoGraph |
Python |
Python Software |
https://www.python.org/ |
R 3.4.1 |
R Core Team, 2016 |
https://www.R-project.org |
t-SNE |
Van Der Maaten and Hinton, 2008 |
https://github.com/jkrijthe/Rtsne |