Sampling time-dependent artifacts in single-cell genomics studies

Massoni-Badosa R; Iacono G; Moutinho C; Kulis M; Palau N; Marchese D; Rodríguez-Ubreva J; Ballestar E; Rodriguez-Esteban G; Marsal S; Aymerich M; Colomer D; Campo E; Julià A; Martín-Subero JI; Heyn H.


Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample acquisition can hinder solid, reproducible results, and a systematic benchmarking is required before entering large-scale data production. Here, we report the existence and extent of gene expression and chromatin accessibility artifacts introduced during sampling and identify experimental and computational solutions for their prevention.

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