GEO series

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

GSE185862 Mus musculus Expression profiling by high throughput sequencing 95 samples Submitted 2021/10/20 Platform GPL24247Platform GPL17021

Summary

The isocortex and hippocampal formation (HPF) in the mammalian brain play critical roles in perception, cognition, emotion and learning. We profiled ~1.3 million cells covering the entire adult mouse isocortex and HPF and derived a transcriptomic celltype taxonomy which includes many new glutamatergic and GABAergic neuron types. Contrary to the traditional view of HPF as having a simpler cellular organization, we discover a complete set of glutamatergic types in HPF homologous to all major subclasses found in the six-layered isocortex, suggesting that HPF and isocortex share a common circuit organization. We also identify large-scale continuous and graded variation of cell types along isocortical depth, across isocortical sheet and in multiple dimensions in hippocampus and subiculum. Overall, our study establishes a molecular architecture of mammalian isocortex and hippocampal formation and begins to shed light on its underlying relationship with the development, evolution, connectivity and function of these two brain structures.

Published in

Yao Z, van Velthoven CTJ, Nguyen TN et al. · Cell 2021 · PMID 34004146 · doi:10.1016/j.cell.2021.04.021

This dataset

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Direct links to NCBI, no account and no request form: the whole study as GSE185862_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 95 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 PRJNA772116 and SRA study SRP341866. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 34004146) ↗

Study design

33 conditions, each sampled once — no replicated groups

VISp_L ×4 ALM_L ×3 SSp_L ×2 MOp_L ×2

Read from the first 40 of 95 sample titles: 33 distinct titles with little repetition. Check it against the sample list below before relying on it.

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