| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological Samples | ||
| Breast carcinoma | Fresh operative tissue samples at MSKCC | N/A |
| Normal breast tissue | Fresh operative tissue samples at MSKCC | N/A |
| Lymph node | Fresh operative tissue samples at MSKCC | N/A |
| Peripheral blood | Patient venipuncture at MSKCC | N/A |
| Antibodies | ||
| anti-CD45 ab | Biolegend | RRID:AB_2566372 |
| DAPI Stain | Calbiochem | SCR_014366 |
| anti-Foxp3 ab | Thermo Fisher | RRID:AB_1834364 |
| anti-CD3 ab | Biolegend | RRID:AB_1575008 |
| anti-CD4 ab | Biolegend | RRID:AB_571945 |
| anti-CD16 ab | Biolegend | RRID:AB_314207 |
| anti-CD56 ab | BD Biosciences | RRID:AB_396853 |
| anti-CD8 ab | Biolegend | RRID:AB_528885 |
| anti-CD19 ab | Biolegend | RRID:AB_2562015 |
| anti-CD11b ab | Biolegend | RRID:AB_2563395 |
| anti-CD45 Y89 | Fluidigm | RRID:AB_2261851 |
| anti-CD235ab | BioLegend | RRID:AB_314620 |
| anti-CD61 | BioLegend | RRID:AB_1227584 |
| anti-CD196/CCR6 Pr141 | Fluidigm | Cat:3141014A |
| anti-CD19 142Nd | Fluidigm | RRID:AB_2651155 |
| anti-CD278/ICOS 143Nd | Fluidigm | Cat:3143025B |
| anti-CD270 144Nd | Fluidigm | Cat:3144022B |
| anti-CD4 145Nd | Fluidigm | RRID:AB_2661789 |
| anti-CD8a 146Nd | Fluidigm | Cat:3146001B |
| anti-CD11c 147Sm | Fluidigm | RRID:AB_2687850 |
| anti-CD14 148Nd | Fluidigm | Cat:3148010B |
| anti-CD127 149Sm | Fluidigm | RRID:AB_2661792 |
| anti-TIGIT | eBioscience | Cat:16-9500-82 |
| anti-CD123 151Eu | Fluidigm | RRID:AB_2661794 |
| anti-CD95/Fas 152Sm | Fluidigm | Cat:3152017B |
| anti-CD45RA 153Eu | Fluidigm | Cat:3153001B |
| anti-TIM3 154Sm | Fluidigm | Cat:3154010B |
| anti-CD39 | BioLegend | RRID:AB_940438 |
| anti-CD274/PD-L1 156Gd | Fluidigm | Cat: 3156026B |
| anti-CD27 158Gd | Fluidigm | Cat: 3158010B |
| anti-CD357/GITR 159Tb | Fluidigm | Cat: 3159020B |
| anti-CD28 160Gd | Fluidigm | Cat: 3160003B |
| anti-CD152/CTLA4 161Dy | Fluidigm | Cat: 3161004B |
| anti-FoxP3 162Dy | Fluidigm | RRID:AB_2687650 |
| anti-CD33 163Dy | Fluidigm | RRID:AB_2687857 |
| anti-CD45RO 164Dy | Fluidigm | Cat: 3164007B |
| anti-CD223/LAG3 165Ho | Fluidigm | RRID:AB_2687859 |
| anti-Ki67 | BD | RRID:AB_396287 |
| anti-CD197/CCR7 167Er | Fluidigm | Cat:3167009A |
| anti-CD154/CD40L 168Er | Fluidigm | Cat: 3170011B |
| anti-CD25 169Tm | Fluidigm | RRID:AB_2661806 |
| anti-CD3 170Er | Fluidigm | RRID:AB_2661807 |
| anti-CD226 171Tb | Fluidigm | Cat: 3171013B |
| anti-CD38 172Yb | Fluidigm | Cat: 3172007B |
| anti-CD137/4–1BB 173Yb | Fluidigm | Cat: 3173015B |
| anti-CD279/PD-1 174Yb | Fluidigm | Cat: 3174020B |
| anti-CD194/CCR4 175Lu | Fluidigm | Cat: 3175021A |
| anti-CD56 176Yb | Fluidigm | RRID:AB_2661813 |
| anti-CD11b 209Bi | Fluidigm | Cat: 3209003B |
| Critical Commercial Assays | ||
| inDrop platform | Custom-built droplet microfluidics platform; Klein et al., 2015; Zilionis et al., 2017. | N/A |
| Microfluidic chips and consumables | Droplet Genomics | https://dropletgenomics.com |
| Chromium Single Cell 5’ Library and Bead Kit | 10× Genomics | cat no. 1000014 |
| HiSeq 2500 | Illumina at MSKCC | N/A |
| NEBNext mRNA Second Strand Synthesis Module | NEB | cat no. E6111S |
| HiScribe T7 High Yield RNA Synthesis Kit | NEB | cat no. E2040S |
| Kapa 2× HiFi HotStart PCR mix | Kapa Biosystems | cat no. KK2601 |
| CyTOF2 | Fluidigm | N/A |
| CyTOF2 Supersampler & Sample Chiller | Victorian Airship & Scientific Apparatus | N/A |
| Indium(III) Chloride | Sigma | Cat: 203440 |
| Maxpar X8 Antibody Labeling Kit 150Nd | Fluidigm | Cat: 201150A |
| Maxpar X8 Antibody Labeling Kit 155Gd | Fluidigm | Cat: 201155A |
| Maxpar X8 Antibody Labeling Kit 166Er | Fluidigm | Cat: 201166A |
| Cell-ID 20-Plex Pd Barcoding Kit | Fluidigm | Cat: 201060 |
| Cell-ID Intercalator-Ir | Fluidigm | Cat: 201192 |
| Cell-ID Cisplatin | Fluidigm | Cat: 201064 |
| FoxP3 Transcription Factor Fix/Perm | eBiosciences | Cat: 00-5523-00 |
| TruStain FcX | BioLegend | Cat: 422302 |
| Deposited Data | ||
| inDrop single-cell RNA-seq dataset | GEO | Accession numbers GSE114727, GSE114725 |
| 10× paired single-cell TCR and RNA-seq dataset | GEO | Accession numbers GSE114727, GSE114724 |
| CyTOF dataset | Flow Repository | https://flowrepository.org/id/FR-FCM-ZYJP |
| Software and Algorithms | ||
| SEQC | This paper | https://github.com/ambrosejcarr/seqc.git |
| Biscuit | This paper and Prabhkaran et al., 2016. | https://github.com/sandhya212/BISCUIT_SingleCell_IMM_ICML_2016 |
| t-SNE | van der Maaten and Hinton, 2008. | https://lvdmaaten.github.io/software/ |
| PhenoGraph | Levine et al., 2015. | https://github.com/jacoblevine/PhenoGraph |
| Diffusion maps | Coifman et al., 2005. | http://www.math.jhu.edu/~mauro/#tab_DiffusionGeom |
| FACSDiva | BD Biosciences | RRID:SCR_001456 |
| FlowJo | BD Biosciences | RRID:SCR_008520 https://www.flowjo.com/ |
| FastQC | Andrews, 2010. | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| STAR 2.5.3a | Dobin et al., 2013. | https://github.com/alexdobin/STAR |
| Edittag | Faircloth and Glenn, 2012. | https://github.com/faircloth-lab/edittag |
| Cell Ranger 2.1.1 | 10× Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest |
| Loupe Cell Browser | 10× Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest#loupetab |
| CyTOF cell debarcoder | Zunder et al., 2015. | https://github.com/nolanlab/single-cell-debarcoder |
| CyTOF Bead Normalization | Finck et al., 2013. |
https://github.com/nolanlab/bead-normalization/ |
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