library_construction_protocol: The isolated intestinal cells were resuspended in digestion buffer and incubated at 37 'C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer. Alive immune cells were sorted using a FACS according to the presence or absence of GFP or Tdtomato signal. Immune cells were washed and resuspended in PBS supplemented with 0.05% BSA. Library was performed according to the manufacter's instructions. Briefly, immune cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gelbead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in everysingle GEM was retrotranscripted to cDNA, which contains an llumina R1 primel sequence, Unique Molecular ldentifier (UMl) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRlselect reagent for subsequent library construction.