Transcriptomic Analysis of Pubertal and Adult Virgin Mouse Mammary Epithelial and Stromal Cell Populations

The mammary gland is a dynamic tissue that mainly develops postnatally under the influence of fluctuating hormone levels. This dataset contains bulk RNAseq data of different mouse mammary gland cell populations (basal, luminal and stromal) that were isolated either during puberty or at different stages of the adult virgin estrous cycle. These data are of interest to researchers in the mammary gland and breast cancer biology field as they allow studies on spatiotemporal, lineage specific changes in gene expression. Overall design: Primary mouse mammary epithelial cell populations were isolated by enzymatic digestion followed by fluorescence activated cell sorting. For the puberty time point, mammary glands were isolated from 34-36 day old FVB/N mice. The 3rd and 4th glands of 4 individual mice from 3 different litters (P34. P35, P36) were isolated, pooled per mouse and processed to single cells. After sorting, the 4 individual samples from each litter were pooled per cell population (resulting in 3 replicate samples of each cell population). Ultimately, 2 replicate samples were used for RNAseq. These replicates were chosen based on RNA quality. For the adult time point, we tracked the estrous cycle of 32 adult FVB/N mice (age distribution 14-16 weeks) every day for at least 10 days to ensure that samples were isolated from mice that were stably cycling. The 3rd and 4th mammary glands were isolated, pooled per mouse and processed to single cells. Adult samples were divided into 'early' and 'late' proestrus, estrous, metestrous and diestrus based on our interpretation of the accompanying vaginal cytology and histology. In case we did not observe a clear difference between early or late stages, we used the cell numbers of the different sorted populations as a second criterium. Ultimately, this resulted in 2 replicates per estrous cycle stage for each of the different cell populations, with each replicate containing the pooled cells from 2 or 3 mice. RNAseq for the puberty and adult timepoints was done in two different runs.