Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor

Crow, M., Paul, A., Ballouz, S., Huang, Z. J., Gillis, J. (February 2018) Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor. Nat Commun, 9 (1). p. 884. ISSN 2041-1723

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DOI: 10.1038/s41467-018-03282-0


Single-cell RNA-sequencing (scRNA-seq) technology provides a new avenue to discover and characterize cell types; however, the experiment-specific technical biases and analytic variability inherent to current pipelines may undermine its replicability. Meta-analysis is further hampered by the use of ad hoc naming conventions. Here we demonstrate our replication framework, MetaNeighbor, that quantifies the degree to which cell types replicate across datasets, and enables rapid identification of clusters with high similarity. We first measure the replicability of neuronal identity, comparing results across eight technically and biologically diverse datasets to define best practices for more complex assessments. We then apply this to novel interneuron subtypes, finding that 24/45 subtypes have evidence of replication, which enables the identification of robust candidate marker genes. Across tasks we find that large sets of variably expressed genes can identify replicable cell types with high accuracy, suggesting a general route forward for large-scale evaluation of scRNA-seq data.

Item Type: Paper
Subjects: organs, tissues, organelles, cell types and functions > cell types and functions
Investigative techniques and equipment > assays > RNA-seq
Investigative techniques and equipment > assays > Single cell sequencing
CSHL Authors:
Communities: CSHL labs > Gillis Lab
CSHL labs > Huang lab
CSHL Cancer Center Program > Gene Regulation and Inheritance Program
Depositing User: Matt Covey
Date: 28 February 2018
Date Deposited: 07 Mar 2018 14:39
Last Modified: 29 Oct 2020 19:01
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