Protocols: SCC9 CIsS, SCC9 4MCisR, SCC9 8MCisR  cells were cultured in cell culture conditions in DMEM-F12 (10%FBS) . Cells were trypsinized and subjected to 10X genomics  for GEM generation. The single cell suspension was converted to single-cell gel beads in the emulsion (GEMs) by using the Chromium Single Cell 5′ Library and Gel Bead kit, and Chromium Single Cell G Chip kit (10x Genomics) according to the manufacturer's protocol scRNA-seq libraries were constructed using a Single Cell 5′ Library and Gel Bead kit, according to manufacturer's protocol. The  cells from SCC9 CIsS, SCC9 4MCisR, SCC9 8MCisR cell types which were tagged using TotalSeq™-C antibodies (C0251, C0252, C0253) respectively.