Table 1.

Single cell datasets of normal mammary and tumour cells.

Reference	Lab	Species	Tissue type (normal/ cancer/ both)	Sample time points	Mammary fraction (epithelial/stroma-immune/both)	Preparation of cells prior to single cell sequencing	Technique + technology	Number of cells/nuclei profiled
Andersson et al. bioRxiv 2020 (preprint)	Lundeberg	Human	Cancer	8x HER2 + breast tumours	Both	Cells spatially selected from fixed tissue sections	Spatial transcriptomics developed by Ståhl et al. Science 2016	1007 spots (where spot refers to a small neighbourhood populated by multiple cells)
Azizi et al. Cell 2018	Pe’er and Rudensky	Human	Both	8x primary breast carcinomas tumour and matched normal breast tissue, peripheral blood and lymph nodes	Stroma-imune	CD45+ FACS sorted cells	scRNA-seq using the inDrop platform	47,016 cells
Bach et al. Nature Comm 2017	Marioni and Khaled	Mouse	Normal	Mammary cells taken during pregnancy (day 14.5), lactation (day 6), involution (day 11) and from virgin 8 week old C57BL/6N mice	Epithelial	Live lineage negative EpCAM+ cells sorted using FACS	scRNA-seq using Chromium 10x Drop-Seq platform	23,184 cells
Bach and Pensa et al. Nature Comm 2021	Khaled and Marioni	Mouse	Both	Tumourogenesis data set: 13 x Blg-Cre; Brca1f/f;p53 + /- mice (aged 30–48 weeks, nulliparous) and 2x C57BL/6N mice (aged 36–40 weeks old)	Both	Viable cells were isolated using MACS Dead Cell Removal Kit	scRNA-seq using Chromium 10x Drop-Seq platform	102,829 cells
				Pregnancy data set: 9x C57BL/6N mice at 4.5/9.5/14.5 days gestation as well as 3x C57BL/6N mice (aged 12 weeks old)
Bartoschek et al. Nature Comm 2018	Pietras	Mouse	Cancer	Tumours from 14 week old MMTV-PyMT mice	Stroma-imune	EpCAM-/CD45-/CD31-/NG2- FACS sorted mesenchymal cells	scRNA-seq using Smart-Seq2	768 cells
Baslan et al. eLife 2020	Hicks	Human	Cancer	Fresh pre-treatment core biopsies were taken from 16 patients’ enroled in phase II clinical trials conducted by the Brown University Oncology Group (BrUOG)	Both	Nuclei was isolated and FACS sorted for ploidy	Single-nuclei copy number analysis developed by Baslan et al. Nature Protocols 2012	Mean of 116 single-nuclei per tumour
Carli et al. J Mammary Gland Biol Neoplasia 2020	Rudolph	Human	Normal	Human milk cells from two participants	Both	Viable cells were isolated using FACS	scRNA-seq using Chromium 10x Drop-Seq platform	3740 cells
Casasent et al. Cell 2018	Edgerton and Navin	Human	Cancer	10x ductal carcinoma in situ (DCIS) and invasive ductal carcinoma (IDC) tumour samples	Both	Cells selected using single cell laser dissection	Topographic single cell sequencing (TSCS, scDNA sequencing)	On average 129 cells per patient
Chung et al. Nature Comm 2017	Park	Human	Cancer	11x tumour cells from different breast cancer subtypes	Both	Dead cells were removed using Ficoll-Paque PLUS	scATAC-seq using the Fluidigm C1 platform	515 cells
Chung et al. Cell Reports 2019	Wahl	Mouse	Normal	Mammary cells from E18 foetal and 8-week old adult CD1 mice	Epithelial	EpCAM+/Lin- FACS sorted cells	snATAC-seq	7846 high quality single nuclei
Engelbrecht and Twigger et al. bioRxiv 2020 (preprint)	Scheel and Khaled	Human	Normal	Mammary tissue from one participant was digested 3 ways (3 h vs. 16 h digest and 10 rpm vs. 100 rpm. shaking speed).	Both	Viable cells were isolated using MACS Dead Cell Removal Kit	scRNA-seq using Chromium 10x Drop-Seq	11,191 cells
Gao et al. Nature Comm 2017	Navin	Human	Cancer	Breast cancer cell lines for technique validation and a single triple negative breast tumour sample	Both	Nuclei isolated from frozen tumour and cell lines	Nanogrid snRNA-seq	796 primary cell nuclei
Giraddi et al. Cell Rep 2019	Wahl and Spike	Mouse	Normal	Mammary cells isolated from day 16/18 embryonic (E16, E18), postnatal day 10 (P10) and 10–16-week-old adult C57BL/6 mice	Epithelial	EpCAM+ FACS sorted cells	scRNA-seq using Chromium 10x Drop-Seq and Fluidigm C1 platforms	6060 cells using 10x and 262 cells using Fluidigm C1
Gkountela et al. Cell 2019	Aceto	Human	Cancer	Blood samples containing circulating tumour cells (CTCs) from 43 patients with progressive breast cancer	Both	Live CTSs were stained for EpCAM, HER2 and EGFR and sorted for CTCs	Single Cell Whole-genome Bisulfite Sequencing developed by Farlik et al. Cell Rep. 2015	89 single CTCs and 71 CTC clusters from patients and xenographs
Grosselin et al. Nature Genetics 2019	Griffiths, Vallot and Gérard	Mouse and Human	Cancer	Patient derived xenogrft mouse models of luminal and treatment resistant breast cancers	Both	Viable cells were isolated using MACS Dead Cell Removal Kit	scChIP-seq and scRNA-seq	2728 cells profiled by scRNA-seq
Han et al. Cell 2018	Guo	Mouse	Normal	Mammary cells taken during pregnancy, lactation, involution and from virgin C57BL/6 mice	Both*	Cells from all major mice organs including mammary gland. *However, no mention was made of removal of the mammary lymph nodes prior to mammary gland dissociation.	scRNA-seq using microwell-seq	61,196 mammary gland cells
Kanaya et al. Commun Biol 2019	Chen	Mouse	Normal	Mammary cells from 9-week-old BALB/cj mice which underwent ovariectomy (surgical menopause) and were treated with vehicle, E2 and/or PBDE	Both	Dead cells were removed using microbeads	scRNA-seq using Chromium 10x Drop-Seq platform	14,856 cells
Karaayvaz et al. Nature Comm 2018	Ellisen	Human	Cancer	6x primary triple negative breast tumours	Both	Viable tumour cells were isolated by FACS sorting	scRNA-seq using Smart-seq2	1189 cells
Knapp et al. Cell Reports 2017	Eaves	Human	Both	7x breast cancer cell lines and 8x normal primary breast tissue samples	Both	N/A	Mass cytometry using 35 markers (16 extracellular and 19 intracellular)	Not disclosed
Li et al. Cell Reports 2020	Brugge	Mouse	Normal	Mammary cells from young (3–4 month, n = 3) and aged (13–14 month, n = 4) old virgin C57BL/6 J mice	Both	None	scRNA-seq using Chromium 10x Drop-Seq platform	13,684 cells
Lo et al. Cancers 2020	Zhou	Mouse	Normal	Mammary cells were isolated from normal and high fat diet (HFD) fed 2 month old C57BL/6 Brca1-/-;p53+/- mice	Stroma-imune	EpCAM- FACs sorted viable stromal and immune cells	scRNA-seq using Chromium 10x Drop-Seq platform	3892 cells
Murrow et al. bioRxiv 2020 (preprint v4)	Gartner	Human	Normal	Mammary cells isolated from 28x premenopausal women of varying BMI and age	Both	Live (DAPI-) cells were sorted using CD31-/CD45-/EpCAM+/-/ CD49f+/- and CD45+	scRNA-seq using Chromium 10x Drop-Seq platform	87,793 cells
Nguyen et al. Nature Comms 2018	Kessenbrock	Human	Normal	Mammary cells isolated from 7x individuals whom underwent reduction mammoplasties	Epithelial	CD31-/CD45- epithelial cells enriched by FACs sorting using CD49f and EpCAM	scRNA-seq using Chromium 10x Drop-Seq and Fluidigm C1 platforms	24,646 cells using 10x and 868 cells using Fluidigm C1
Pal et al. Nature Comms 2017	Visvader	Mouse	Normal	Mammary cells were isolated from early postnatal (2 week old), mid-pubertal (5 weeks old) and mature adult (10 weeks, either from virgin or pregnant) FVB/NJ mice	Epithelial	CD45-/CD31-/CD24+ epithelial cells were FACS enriched	scRNA-seq using Chromium 10x Drop-Seq and Fluidigm C1 platforms	3308 cells using 10x and 460 cells using Fluidigm C1
Pervolarakis et al. Cell Reports 2020	Watanabe and Kessenbrock	Mouse	Normal	Mammary cells were isolated from 10-week-old FVB/NJ mice	Both	FACS sorting using markers CD31, CD45, EpCAM and CD49f separated live cells for scRNA-seq and basal/luminal cells for scATAC-seq	scRNA-seq and scATAC-seq was performed using 10x Genomics Chromium platforms	26,859 cells were profiled using scRNA-seq and 23,338 cells were profiled using scATAC-seq
Salmén et al. bioRxiv 2018 (preprint)	Lundeberg	Human	Cancer	Tumour tissue sections from 10 patients diagnosed with HER2 + breast cancer	Both	N/A	Spatial Transcriptomics developed by Ståhl et al. Science 2016 and others	1007 spatial spots
Sebastian et al. Cancers 2020	Loots	Mouse	Cancer	Mammary cells were extracted from 10-week-old BALB/c mice with 4T1 derived mammary tumours (a synergistic model for triple negative breast cancer)	Stroma	Using magnetic cell separation, CD45 depleted or CD45/CD90.1 depleted cells were sequenced, as well as bulk cells and CD140a+/EpCAM-/CD45-/7AAD- FACS sorted fibroblasts.	scRNA-seq using Chromium 10x Drop-Seq platform	6420 cells
Sun et al. J. Biol. Chem. 2018	Deng	Mouse	Normal	Mammary cells were isolated from 3 to 4 month-old virgin or day 12.5 pregnant FVB mice	Epithelial	Lineage positive (Lin+, endothelial or immune) cells were excluded using the EasySeq mouse epithelial cell enrichment kit. Luminal and basal cells were FACS sorted for using CD24 and CD29	scRNA-seq using Fluidigm C1 platform	239 cells
Thong et al. Front. Cell Dev. Biol. 2020	Colacino	Human	Normal	Mammary cells were isolated from 3x normal mammoplasty tissue samples. Additionally, mammary cells from the 3 patients were conditionally reprogrammed in vitro and also sequenced.	Both	None	scRNA-seq using drop-seq protocols developed by Macosko et al. 2015.	Not disclosed
The Tabula Muris Consortium Nature 2020	–	Mouse	Normal	Mammary cells taken from at 3, 18 and 21 months from C57BL/6JN mice	Both*	Cells from all major mice organs including mammary gland. *However, no mention was made of removal of the mammary lymph nodes prior to mammary gland dissociation.	scRNA-seq using Chromium 10x Drop-Seq platform	15,577 mammary cells
Tognetti et al. bioRxiv 2020 (preprint)	Bodenmiller	Human cell lines	Both	62x breast cancer cell lines and 5x normal cell lines	N/A	N/A	Mass cytometry using 34 markers	> 80 million cells
Twigger et al. bioRxiv 2020 (preprint)	Khaled and Scheel	Human	Normal	4x samples from participants donating mammoplasty tissue and 4x human milk samples from lactating women	Both	None	scRNA-seq using Chromium 10x Drop-Seq platform	24,666 non-lactating breast cells and 27,023 human milk cells
Vatter et al., Cell Reports 2018	Bodenmiller, LaBarge and Lorens	Human	Normal	57 samples were profiled consisting of cultured cells from 44 women and 13 uncultured breast epithelia samples.	Epithelia	N/A	Mass cytometry using 29 markers	880,000 cells
Wagner at al. Cell 2019	Bodenmiller	Human	Both	144x human breast tumours and 50x normal breast tissue samples	Both	N/A	Mass cytometry using 73 markers	26 million cells
Wang et al. eLife 2020	Schwertfeger	Mouse	Normal	Mammary cells isolated from 10-week-old dioestrus FVB/NJ mice	Stroma-imune	CD45+ cells were enriched for using magnetic cell separation	scRNA-seq using Chromium 10x Drop-Seq platform	13,000 cells were targeted
Wu et al. EMBO J 2020	Swarbrick	Human	Cancer	5x triple negative breast tumours	Both	Viable cells were enriched for using EasySep Dead Cell Removal Kit	scRNA-seq using Chromium 10x Drop-Seq platform	24,271 cells
Wuidart et al. Nat Cell Biol 2018	Blanpain	Mouse	Normal	Mammary cells were isolated from embryonic day 14 (E14) and > 8-week-old adult mice	Epithelial	Embryonic CD49fHi/Lgr5Hi cells, adult CD24+/CD29Hi basal and adult CD24+/CD29Lo luminal cells were FACS enriched	scRNA-seq using Smart-seq2	193 cells