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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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journal contribution
posted on 04.05.2022, 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.

Funding

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).

History

Publication Date

01/01/2022

Journal

Scientific Data

Volume

9

Issue

1

Article Number

ARTN 96

Pagination

9p.

Publisher

Springer Nature

ISSN

2052-4463

Rights Statement

© The Author(s) 2022. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.