Fig. 1

Single Cell Implementation to Find Expression of Retrotransposons (SCIFER) incorporates information from visually validated bulk RNA-Seq to accurately measure L1 mRNA expression in scRNA-Seq datasets. A. The SCIFER method workflow is shown. Single cells are sequenced and demultiplexed using 10X Genomics cellranger tools (1). Reads are labeled with their corresponding barcode, reads are aligned uniquely to the reference genome, PCR duplicates are removed by alignment and UMI, alignments are strand separated, and alignments are compared to a list of authentically expressed L1 loci from a bulk RNA-Seq dataset in a matched sample (2). Reads are aligned using 10x Genomics and gene expression is quantified using Seurat (3). B. A table showing the number of cells captured per dataset, the average number of genomic aligned reads using the tryhard bowtie settings per cell (see Methods), and the number of cells with an assigned cell type per dataset. Values are listed for datasets: MCF7 High coverage, MCF7 Low coverage [44], Mouse Testis 1 and 2 [37], and Human Testis 24 yo and 25 yo donors [35]