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

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 expres...

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Detalles Bibliográficos
Autores principales: Chen, Yunshun, Pal, Bhupinder, Lindeman, Geoffrey J., Visvader, Jane E., Smyth, Gordon K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8943201/
https://www.ncbi.nlm.nih.gov/pubmed/35322042
http://dx.doi.org/10.1038/s41597-022-01236-2
Descripción
Sumario: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.