Study: CD4+ T effector cells in the colon lamina propria, several infections (10X) 7107 cells

CD4+ T effector cells lymphocytes (Teff) are functionally heterogeneous, and traditionally divided into subsets defined by the cytokines they produce. To determine the actual states that Teff adopt in frontline tissues in vivo, we applied single-cell RNAseq on colonic Teff in a range of conditions: germfree, unchallenged Specific Pathogen Free, or after bacterial infection with Citrobacter rodentium or attenuated Salmonella typhimurium, or two helminths Heligmosomoides polygyrus and Nippostrongylus brasiliensis . We chose infection times that allowed responses to develop fully and achieve full Teff bias (day 11-13), and the pathogens elicited the expected biased cytokine responses. CD4+ cells from control or infected mice were hashtagged with DNA-coded antibodies and comingled for sorting, microfluidic encapsulation and library construction, yielding highly congruent data.