Bioinformatics Seminar
Time:
Venue: 11AM
31 August 2021
Zoom WebinarUnderstanding cell lineage commitment and breast cancer development by single cell RNA-seq
Jinming ChengWEHI Bioinformatics
Breast cancer is the most common cancer and the leading cause of cancer death in women worldwide. Almost all breast cancers arise from the terminal duct lobular units of the mammary duct system. To understand the genesis and development of breast cancer, one key step is to understand the cell lineage commitment mechanism of normal mammary duct epithelium.
In this study, we took advantage of the single cell RNA-seq technology to investigate normal epithelial cells of mouse mammary gland at different ages (embryonic, early post-natal, pre-puberty, puberty, and adult). The datasets used in our study were obtained from the publicly available Gene Expression Omnibus database. The popular Seurat package as well as our ternary plot method were used for the analyses of the single cell RNA-seq data from 10X genomics and Fluidigm C1 platforms, and we compared our ternary plot method with the Seurat method. In addition, we simply compared the performance of different doublet prediction methods and chose the best one for our single cell data analysis.