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

Moderated experimental designs can effectively balance batch-effect reduction and cell loss, with cell loss doubling for each additional hashtag used in single-cell experiments.

• Why it matters: Reducing batch effects is crucial for accurate single-cell data, but current hashtag-assisted pooling can lead to significant cell loss, impacting data quality and interpretation.
• What they did: The study evaluated four alternative designs—compound, reference, chain, and confounded—quantifying batch effects and cell loss across different configurations, revealing a linear relationship between hashtags and cell loss.
• The result: Findings show the reference design offers optimal performance, enabling researchers to select strategies that best mitigate batch effects while preserving cell numbers for their specific biological questions.