Identity crisis: exploring the boundaries of cell type identification in the age of single-cell transcriptomics.

Overview

1. Institute for Neurophysiology, Charité Universitätsmedizin—Berlin, Berlin, Germany

Abstract

The rise of single-cell transcriptomics and comprehensive reference atlases promised a unifying molecular framework to classify cell identity. Yet transcriptomic identities are often interpreted outside the environmental contexts in which they arise. Here, we analyzed primary cortical cultures, which lack native tissue architecture, to compare their transcriptional profiles to multiple in vivo mouse cortical reference datasets. We found that while core molecular signatures for major neuronal subclasses are largely preserved in vitro, the loss of in vivo structure triggers high transcriptional divergence associated with metabolic and physiological state. We also identified clusters that consistently show low confidence in the classification tool. These ambiguous populations express incomplete canonical marker profiles resulting from a lack of structural cues necessary for full maturation. These observations suggest that while transcriptomic reference frameworks capture major aspects of neuronal identity, their interpretation can become less certain when cells are profiled outside their native environment. Our findings highlight the importance of considering environmental context when interpreting transcriptome-based cell type annotations and provide a resource for understanding how neuronal transcriptional programs are reshaped in vitro.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Data

Datasets cited

• zenodo:19554693, at Zenodo; found in “Data availability statement”

Data availability statement

Publicly available datasets were analyzed in this study. Raw and processed snRNA-seq data reported in this study are publicly available on the Zenodo repository at Doi: 10.5281/zenodo.19554693 (https://doi.org/10.5281/zenodo.19554693).

Reproduced under the paper's license (CC BY), from the paper cited above.

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Version 2, 28 September 2026

• Funding: added Einstein Stiftung Berlin

Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 4 authors, 5 keywords, 44 references.

Cite

This paper

Yang, S., Tyagi, S., Rosenmund, C., & Herman, M. A. (2026). Identity crisis: exploring the boundaries of cell type identification in the age of single-cell transcriptomics. Frontiers in cellular neuroscience, 20, 1819116. https://doi.org/10.3389/fncel.2026.1819116

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