Spike_in_addition_in_single_cell_RNA_seq_with_trophoblast_stem_cells

Single-cell RNA sequencing (scRNA-seq) is a powerful technique for studying transcriptional activity in individual cells. However, it is susceptible to cell-specific biases that confound comparisons of expression levels between cells. One approach to removing these biases is spike-in normalization, where counts are scaled to remove differences between cells in the coverage of known spike-in transcripts. This approach assumes that the same amount of spike-in RNA is added to each cell, which may not be true at the single-cell level. In this experiment, we aim to test this assumption by adding mixtures of different spike-ins to each cell, and computing the log-ratio of the total counts between spike-ins for each cell, and estimating the variance of the log-ratio across cells.