GEO series

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

GSE85755 Danio rerio; Mus musculus Expression profiling by high throughput sequencing 21 samples Submitted 2017/09/28 Platform GPL19057Platform GPL20828

Summary

In many gene expression studies, cells are extracted by tissue dissociation and Fluorescence-Activated Cell Sorting (FACS), but the effect of these protocols on cellular transcriptomes is not well characterized and often ignored. Here, we applied single-cell mRNA sequencing (scRNA-seq) to muscle stem cells, and unexpectedly found a subpopulation that is strongly affected by the widely-used dissociation protocol that we employed. One implication of this finding is that several published transcriptomics studies may need to be reinterpreted. Importantly, we detected similar subpopulations in other single-cell datasets, suggesting that cells from other tissues might be affected by this artefact as well.

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Direct links to NCBI, no account and no request form: the whole study as GSE85755_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 21 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA339266 and SRA study SRP082370. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28960196) ↗

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