Sampling time-dependent artifacts in single-cell genomics studies

Genome Biol. 2020 May 11;21(1):112. doi: 10.1186/s13059-020-02032-0.


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.

Keywords: Benchmarking; Biobank; CLL; Chronic lymphocytic leukemia; Cryopreservation; PBMC; Peripheral blood mononuclear cells; RNA sequencing; Sampling; Single-cell.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Artifacts*
  • Cryopreservation
  • Epigenome
  • Female
  • Genomics*
  • Humans
  • Leukocytes, Mononuclear
  • Male
  • Single-Cell Analysis*
  • Time Factors
  • Transcriptome