LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [scRNA-seq]

In this study, we investigated LINE1 (L1), a major family of transposon elements (TEs) in the human genome, in naive hES cells for its roles in regulating 8-cell (8C) stage-specific totipotent genes. We performed single-cell RNA-seq (scRNA-seq) to assess if L1 knockdown in RSeT+DT naive hES cells induces 8-cell-like cells (8CLCs), and profile the transcriptome changes in the cells. Overall design: RSeT media maintained naive H9 hES cells were transfected with 6-FAM (Fluorescein) labeled SO-L1 and ASO-L1 oligos and cultured in the RSeT+DT condition. 48 hours later, 100,000 FAM+ cells were FACS collected and immediately processed on the 10x Genomics Chromium platform using the Single Cell 3' v3 RNA-seq kit and targeting a yield of 12,000 cells. Final libraries were sequenced on a NovaSeq6000 S1 flow cell (Illumina) to an average depth of >65,000 reads/cell.