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R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue

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posted on 2022-05-04, 04:49 authored by Y Chen, Bhupinder PalBhupinder Pal, GJ Lindeman, JE Visvader, GK Smyth
Breast cancer is a common and highly heterogeneous disease. Understanding cellular diversity in the mammary gland and its surrounding micro-environment across different states can provide insight into cancer development in the human breast. Recently, we published a large-scale single-cell RNA expression atlas of the human breast spanning normal, preneoplastic and tumorigenic states. Single-cell expression profiles of nearly 430,000 cells were obtained from 69 distinct surgical tissue specimens from 55 patients. This article extends the study by providing quality filtering thresholds, downstream processed R data objects, complete cell annotation and R code to reproduce all the analyses. Data quality assessment measures are presented and details are provided for all the bioinformatic analyses that produced results described in the study.


This work was supported by the Chan Zuckerberg Initiative (EOSS4 grant number 2021-237445), the National Breast Cancer Foundation (NBCF, IIRS-20-022), Australian National Health and Medical Research Council (NHMRC) grants (#1054618, 1100807,1113133, 1153049); NHMRC IRIISS; the Victorian State Government Operational Infrastructure Support; the Australian Cancer Research Foundation and the Ian Potter Foundation. G.J.L., G.K.S. and J.E.V. were supported by NHMRC Fellowships (G.J.L. #1078730 and 1175960; G.K.S. #1058892; J.E.V. #1037230 and 1102742); Y.C was supported by Medical Research Future Fund (MRFF) Investigator Grant (#1176199).


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