Single-cell full-length RNA-sequencing of MCF7 and BT-474 cells using down-scaled Smart-seq2

We report single-cell RNA-sequencing data of wild type, breast cancer cells MCF7 and BT-474. Single cells were isolated using the F.SIGHT single cell dispenser. cNDA synthesis and library preparation were down-scaled to 1/10 of original reaction volumes. By comparative UMAP clustering we could show that our MCF7-cluster exactly overlapped with sequencing data from GSE151334. Data was analyzed using three common alignment tools: salmon, kallisto and STAR. DE analysis was performed with inputs from each aligner. We proved the overexpression of ErbB2 in BT-474 compared to MCF7 in all cases. After single cell isolation of MCF7 and BT-474 cells with the F.SIGHT, cDNA synthesis (Smart-seq2) and library preparation (Nextera XT) were performed at 1/10 of original reaction volumes.