Acquisition, processing, and single-cell analysis of normal human breast tissues from a biobank

Poornima Bhat-Nakshatri; Natascia Marino; Hongyu Gao; Yunlong Liu; Anna Maria Storniolo; Harikrishna Nakshatri

doi:10.1016/j.xpro.2021.101047

Acquisition, processing, and single-cell analysis of normal human breast tissues from a biobank

STAR Protoc. 2021 Dec 16;3(1):101047. doi: 10.1016/j.xpro.2021.101047. eCollection 2022 Mar 18.

Authors

Poornima Bhat-Nakshatri¹, Natascia Marino², Hongyu Gao³, Yunlong Liu^{3

4}, Anna Maria Storniolo^{2

4}, Harikrishna Nakshatri^{1

5

4

6}

Affiliations

¹ Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
² Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
³ Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
⁴ Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
⁵ Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
⁶ Richard L. Roudebush VA Medical Center, Indianapolis, IN 46202, USA.

Abstract

The Komen Tissue Bank is the only biorepository in the world for normal breast tissues from women. Below we report the acquisition and processing of breast tissue from volunteer donors and describe an experimental and analysis pipeline to generate a single-cell atlas. This atlas is based on single-cell RNA-seq and is useful to derive breast epithelial cell subcluster-specific gene expression signatures, which can be applied to breast cancer gene expression data to identify putative cell-of-origin. For complete details on the use and execution of this protocol, please refer to Bhat-Nakshatri et al. (2021).

Keywords: Cancer; Cell Biology; Gene Expression; Genomics; Health Sciences; Molecular Biology; RNAseq; Sequence analysis; Single Cell.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biological Specimen Banks
Breast / metabolism
Breast Neoplasms* / genetics
Female
Humans
Single-Cell Analysis*
Transcriptome