High coverage single cell RNA-Seq of pooled MCF7 and HEK293-ZRT cells to discover expression patterns of the LINE1 retrotransposon

We performed high coverage scRNA-Seq on a pool of MCF7 and HEK293-ZRT cells in a 9:1 ratio, respectively, using a total of 853 cells in this experiment. Detection of mobile element expression at the locus-specific level requires high sequencing depth. Here, MCF7 and HEK293-ZRT single cells have been sequenced to a sufficient level to quanitfy LINE1 expression in single cells and compare expression differences between individual cells. Single-cell RNA sequencing was carried out on individual cells using the 10X Genomics Chromium™ Single Cell 3' Library & Gel Bead Kit v3 and 150 cycle kit. 750 cells were targeted for sequencing. Overall design: scRNA-Seq of MCF7 and HEK293-ZRT cells with a combined total of 853 cells. HEK293-ZRT cells were used as an internal control to test for accurate cell clustering. HEK293-ZRT cell identiity was confirmed by aligning reads to the ZRT transgene sequence. Raw reads were demultiplexed using 10X Genomics bcl2fastq command. Gene expression analysis was performed using 10X Genomics cellranger.