Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments

Minimizing experimental noise is integral to robust data generation in single-cell science. Experimental processing of different samples as a single pool, made possible by hashtag-assisted pooling, helps minimize batch-effects, but the computational demultiplexing of the data can also lead to loss of cells whose hashtags cannot be resolved accurately. Here, we examine four alternate experimental designs that could be used instead of a single-pool approach and quantify the batch effects as well as cell loss in each case. While a reference design offers the best performance, this study can help individual investigators choose one suited for their biological questions.