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 manufacturers instructions, and sequenced on an Illumina Nextseq1000 platform (NextSeq 1000/2000 P2 reagents (100 cycles)).