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

GSE185862 Mus musculus (mouse) RNA-seq (gene expression) 95 samples Submitted 2021/10/20 Platform GPL24247Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 95 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
95 samples: 83 distinct titles, 5 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
A taxonomy of transcriptomic cell types across the isocortex and hippocampal formationCell · 2021
Summary (written by the submitters)
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.
Read the full summary ↓
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
A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation
Yao Z, van Velthoven CTJ, Nguyen TN et al. · Cell 2021 · PMID 34004146 · doi:10.1016/j.cell.2021.04.021
This dataset
Open GSE185862 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE185862_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

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
83 distinct titles, 5 of them repeated
VISp_L ×5 SSp_L ×4 ALM_L ×3 MOp_L ×3 ACA_L ×2

How we read this: Read from 95 sample titles: 83 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 55 more — browse all 95 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.