Sampling time-dependent artifacts in single-cell genomics studies
Ramon Massoni-Badosa, Giovanni Iacono, Cátia Moutinho, Marta Kulis, Núria Palau, Doménica Marchese, Javier Rodríguez‐Ubreva, Esteban Ballestar, Gustavo Rodríguez-Esteban, Sara Marsal, Marta Aymerich, Dolors Colomer, Elı́as Campo, Antonio Julià, José I. Martín‐Subero, Holger Heyn
Abstract
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.