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

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

本数据集包含了经过处理的基因表达（计数）单细胞RNA测序数据，该数据涉及与癌症及免疫细胞共培养的细胞在 trifluridine 和 DMSO 对照剂处理下的两个时间点（12小时和72小时）的实验结果。HCT116 细胞以 50,000 个细胞/3mL/孔的密度接种于 6 孔 Nunc 培养皿中，并在添加 PBMCs 细胞前进行 24 小时的预培养，PBMCs 细胞以 1:8 的比例加入。共培养细胞分别用 DMSO 车辆组（0.1%）或 FTD（3mM）处理 12 小时或 72 小时。对于处理 72 小时的细胞，按照制造商的说明使用 MACS Dead Cell Removal Kit（Miltenyi Biotec，Gladbach，德国）以提高样本的存活率，以便进行 RNA 测序。12 小时处理的样本由于存活率已足够，未进行死细胞去除。所有样本均用含 0.04% BSA 的 PBS 溶液（2x1mL）洗涤。Chromium Next GEM 单细胞 3' 基因组库制备和 RNA 测序由瑞典乌普萨拉大学的生命科学实验室（Science for Life Laboratory）国家基因组学基础设施（NGI）的 SNP&SEQ 技术平台执行。该数据集包含了使用 10x Genomics 提供的 Cell Ranger 工具包版本 5.0.1 处理的数据，用于解复用、将读段对齐至人类参考基因组 GRCh38，并生成基因-细胞独特的分子标识符。