Single_cell_RNA_seq_and_bisulfite_seq_at_various_stares_of_HiPSCs_differentiating_toward_definitive_endoderm_derived_lineages

When comparing the differentiation capacities of pluripotent stem cell lines that have different genetic backgrounds, batch to batch experimental variablility poses a significant challenge, especially when trying to identify smaller effects. One way to address this issue is to differentiate several different lines in the same culture dish, thereby elimating experimental variation. In addition, it allows researchers to analyze many more lines with less experiments. Parallel single cell RNA-Seq and bisulfite sequencing exploits that individual cells are tagged and hence each cell canbe reliably assigned to the donor of origin based on the genetic variants it contains. In addition, analyzing the genetic signature of single cells within a differentiating population can reveal differentation stages that are not easily detected in bulk RNAseq data. Studying the transcriptome (RNA-seq) and DNA methylation (bisulfite-seq) from the same cell allows detailed comparison of expression and epigenetic effects.