The challenges of single cell transcriptomics on difficult human tissue: the placenta

We focus on the placenta, a challenging tissue to transcriptomically interrogate due to senescence, intermittent hypoxia, high levels of RNase activity and tissue trauma at delivery. We performed single cell and nuclei transcriptomics on two samples with probe-based and native molecule transcript capture, droplet based and in situ plate based cell isolation.

We explored sample and storage variations, including freshly dissociated tissues, fixed cells, snap frozen and FFPE processing. We find that variations in sample processing and storage have much larger effect on cell type proportions than differences in chemistry, impacting the biology that can be learned or the identification of disease markers. Further, the transcriptomic output of in situ combinatorial indexing consistently overlaps, with single nucleus transcriptomics, sharing little with other modalities.