Rxivist logo

Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows

By Elena Denisenko, Belinda B. Guo, Matthew Jones, Rui Hou, Leanne de Kock, Timo Lassmann, Daniel Poppe, Olivier Clement, Rebecca K. Simmons, Ryan Lister, Alistair R. R. Forrest

Posted 06 Nov 2019
bioRxiv DOI: 10.1101/832444 (published DOI: 10.1186/s13059-020-02048-6)

Single-cell and single-nucleus RNA sequencing have been widely adopted in studies of heterogeneous tissues to estimate their cellular composition and obtain transcriptional profiles of individual cells. However, the current fragmentary understanding of artefacts introduced by sample preparation protocols impedes the selection of optimal workflows and compromises data interpretation. To bridge this gap, we compared performance of several workflows applied to adult mouse kidneys. Our study encompasses two tissue dissociation protocols, two cell preservation methods, bulk tissue RNA sequencing, single-cell and three single-nucleus RNA sequencing workflows for the 10x Genomics Chromium platform. These experiments enable a systematic comparison of recovered cell types and their transcriptional profiles across the workflows and highlight protocol-specific biases important for the experimental design and data interpretation.

Download data

  • Downloaded 3,887 times
  • Download rankings, all-time:
    • Site-wide: 1,249 out of 93,254
    • In genomics: 264 out of 5,873
  • Year to date:
    • Site-wide: 994 out of 93,254
  • Since beginning of last month:
    • Site-wide: 4,018 out of 93,254

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News