title: EpCAM TCB induces temporal dependent immune cell state changes in IIOs unleashing their cytotoxic capability compared to donor-matched control cultures
design: EpCAM TCB induces temporal dependent immune cell state changes in IIOs unleashing their cytotoxic capability compared to donor-matched control cultures
library_construction_protocol: All the samples were dissociated as follows: organoid domes were dislodged and mechanically broken up and transferred to 1% BSA-coated tubes. The organoid fragments were centrifuged at 400g, 4min, RT. The supernatant was removed and the enzymes of the neural tissue dissociation kit (Miltenyi Biotec) were mixed in HBSS-1%BSA buffer. The organoid fragments were dissociated to single cells for a total of 30 min with thorough pipetting every 7 minutes. Next, cells were filtered through a 40 µM filter and single cells were centrifuged at 450g, 4min, RT. Dead cells and EpCAM+ cells were magnetically removed and the cell pellets containing only viable immune cells were subsequently resuspended in DPBS 1% BSA. Nuclei acid extraction protocol was performed according to the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index), CG000315, Rev E.  The kit used was: Chromium Next GEM Single Cell 3' Kit v3.1, 16 rxns PN-1000268. Library Construction protocol was performed according to the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index), CG000315, Rev E.  The kit used was: Library Construction Kit 16 rxns PN-1000190.