Here we share how we processed all our samples for the Human Breast Cell Atlas project. This is by no means a definitive protocol but it is the one that works for us after nearly 12 months of optimization working with Breast Cancer Now Tissue Bank. We accept no responsibility and please use at your own discretion. Good luck!

The final version of the HBCA can be found in the paper published in Nature Genetics:

A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast

Austin D. Reed*, Sara Pensa*, Adi Steif, Jack Stenning, Daniel J. Kunz, Linsey J. Porter, Kui Hua, Peng He, Alecia-Jane Twigger, Abigail J. Q. Siu, Katarzyna Kania, Rachel Barrow-McGee, Iain Goulding, Jennifer J. Gomm, Valerie Speirs, J Louise Jones, John C. Marioni & Walid T. Khaled 

Nat Genet 56, 652–662 (2024). https://doi.org/10.1038/s41588-024-01688-9

The processed data from our own study (800,000 cells) as well as the integrated HBCA (2.1M cells) can be explored at CellxGene. Please reference the paper if you use this data for your studies.