Mammary intraepithelial lymphocytes promote lactogenesis and offspring fitness

T cells accumulate in the mammary gland during pregnancy and lactation. In order to understand the diversity, transcriptional states, TCR repertoire, and function of mammary gland T cells, and how these change during pregnancy and lactation compared to homeostasis, we performed single cell RNA sequencing on mammary gland T cells in mice. Mammary T cells from nulliparous, pregnant (G18.5), and lactating (L5) mice were sorted from samples labeled with TotalSeqC hashtags antibodies (Biolegend) using a Sony MA900 sorter. Sorted cells were pooled and 42000 cells per lane (total of 8 lanes) were loaded on a Chromium Single Cell Controller (10X Genomics) to encapsulate the cells into droplets. The gene expression (GEX), hashtag oligonucleotide (HTO) and VDJ (TCR) sequencing libraries were prepared using Chromium Single Cell 5’ v2 reagent kits following the manufacturer’s instructions, and sequenced on an Illumina Nextseq1000 platform (NextSeq 1000/2000 P2 reagents (100 cycles)).