GSM5224056: CD103+DC_gut_CD11a.KO_R3; Mus musculus; RNA-Seq
Cells were isolated from C57BL/6 mice that previously underwent complete mesenteric lymphadenectomy. ILCs were identified as live, single, CD45+ IL-7Rα+ lineage- (CD3, CD5, CD11b, CD11c, B220) cells and T cells as live, single, CD45+ CD11b- CD11c- B220- CD3+ CD5+ CD4+ CD44high CD25- cells. Cells for RNA seq were purified by flow cytometric sorting, collected into 350 μl RLT plus buffer (Qiagen) and stored at -80°C until further processing. Samples were sorted in quadruplicates and isolated cell types included migratory ILCs (n = 15) and T cells (n = 8) from afferent lymph of thoracic duct cannulated mice in steady state, ILCs (n = 4) and T cells (n = 4) from the colonic and small intestinal lamina propria at similar proportions, and migratory ILCs (n = 25) from afferent lymph of Salmonella infected mice that underwent thoracic duct cannulation. RNA was isolated according to the manufacturer's protocol (RNeasy plus micro kit, Qiagen). CD11b+ CD103- and CD11b+ CD103+ DCs (live, single, CD45+, CD64- MHCIIhigh CD11c+) were isolated from the small intestinal lamina propria of C57BL/6 mice after removal of Peyer's Patches. The migratory DC counterparts were isolated by thoracic duct cannulations of mice that previously underwent complete mesenteric lymphadenectomy. RNA was isolated according to the manufacturer's protocol (RNeasy kit, Qiagen). Libraries were prepared using the Smart-seq v4 ultra-low input kit (Takara Bio, Kusatsu, Japan). Samples were sequenced to a mean depth of 37.5 million read pairs per sample using a HiSeq4000 (Illumina, San Diego, California, USA). The read length was 75bp.
GEO Accession
GSM5224056