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Single-cell gene expression count data for trifluridine treated co-culture of tumor cell line with PBMC

dataset
posted on 21.06.2022, 09:16 authored by Claes AnderssonClaes Andersson, Tove Selvin

Gene expression (counts) scRNA-seq of co-cultured cancer- and immune cells treated with trifluridine and DMSO control assayed at two time-points (12h and 72h).


HCT116 were seeded in 6-well Nunc plates (50,000 cells/3mL/well) and precultured for 24 h before PBMCs were added at a 1:8 ratio. Co-cultures were treated with DMSO vehicle (0.1%) or FTD (3mM) for 12 h or 72 h. MACS Dead Cell Removal Kit (Miltenyi Biotec, Gladbach, DEU) was performed according to the manufacturer’s instructions on cells treated for 72 h to increase the viability of the samples before RNA-sequencing. The viability of the samples treated for 12 h was not subjected to Dead Cell Removal as the viability was already sufficient. All samples were washed in PBS with 0.04% BSA (2x1mL). Chromium Next GEM Single Cell 3’ library preparation and RNA-sequencing were performed by the SNP&SEQ Technology Platform (National Genomics Infrastructure (NGI), Science for Life Laboratory, Uppsala University, Sweden). 


This data set contains processed data using Cell Ranger toolkit version 5.0.1 provided by 10x Genomics,  for demultiplexing, aligning reads to the human reference genome GRCh38, and generating gene-cell unique molecular identifiers 

Funding

Lions Cancer Research Fund

History

Publisher

Uppsala University