by Amanda A. G. Ferreira, Sergio Córdoba, Raghuvanshi Rajesh, Ben Jiwon Choi, Claude Desplan Glial cells are essential for proper nervous system development and function. To understand glial development and function, we comprehensively annotated the glial cells from two large single-cell mRNA-sequencing (scRNA-seq) atlases of the developing Drosophila visual system. This allowed us to identify all glial cell types from larval to adult stages and follow their developmental trajectories to understand how the diversity of glial types is generated during development. We show that whereas most glial types, such as chiasm glia, gradually change their transcriptome as they mature during development, neuropil glia that transcriptionally appear as a single-cell class in larvae, splits into ensheathing (EG) and astrocyte-like (ALG) glia types during pupal stages. We have experimentally validated these developmental trajectories and identified the genetic markers expressed through the differentiation between EG and ALG classes. Unexpectedly, our analysis of scRNA-seq datasets allowed us to discover that the transcriptome of glial cell bodies can be distinguished from that of their processes. We have identified that processes are enriched for distinct mRNAs that were validated in vivo. This work provides the most detailed transcriptomic analysis of optic lobe glia during development and helps explain the expansion of glial diversity observed in the adult visual system. We also present an innovative computational approach to identify mRNA species that are differentially localized to cell bodies or cellular processes.

Scientists at Earlham Institute, John Innes Centre, University of Freiburgh, and University Medical Center Rotterdam present EISCA and EISTA, two standardized, end-to-end pipelines for single-cell RNA- seq and imaging-based spatial transcriptomics analysis.

by Amanda A. G. Ferreira, Sergio Córdoba, Raghuvanshi Rajesh, Ben Jiwon Choi, Claude Desplan Glial cells are essential for proper nervous system development and function. To understand glial development and function, we comprehensively annotated the glial cells from two large single-cell mRNA-sequencing (scRNA-seq) atlases of the developing Drosophila visual system. This allowed us to identify all glial cell types from larval to adult stages and follow their developmental trajectories to understand how the diversity of glial types is generated during development. We show that whereas most glial types, such as chiasm glia, gradually change their transcriptome as they mature during development, neuropil glia that transcriptionally appear as a single-cell class in larvae, splits into ensheathing (EG) and astrocyte-like (ALG) glia types during pupal stages. We have experimentally validated these developmental trajectories and identified the genetic markers expressed through the differentiation between EG and ALG classes. Unexpectedly, our analysis of scRNA-seq datasets allowed us to discover that the transcriptome of glial cell bodies can be distinguished from that of their processes. We have identified that processes are enriched for distinct mRNAs that were validated in vivo. This work provides the most detailed transcriptomic analysis of optic lobe glia during development and helps explain the expansion of glial diversity observed in the adult visual system. We also present an innovative computational approach to identify mRNA species that are differentially localized to cell bodies or cellular processes.

Proceedings of the National Academy of Sciences, Volume 123, Issue 39, September 2026. SignificanceUnderstanding how gene expression dynamically evolves in vivo is essential for interpreting cellular behavior in complex tissues, yet conventional scRNA-seq captures only static transcript levels. Kinetics-seq overcomes this limitation by ...

The authors present a framework to isolate condensed marker gene signatures by requiring both conserved cell-type specificity and conserved expression across multi-species scRNA-seq datasets. Bone mar...