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Enhancer-AAVs allow genetic access to diverse populations of astrocytes and oligodendrocytes across species

GSE235987 Mus musculus (mouse) Single-cell RNA-seq 2040 samples Submitted 2024/06/26 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 2040 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
2040 samples: 14 conditions, mostly with about 38 replicates eachGroups 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.
Summary (written by the submitters)
Proper brain function requires the assembly and function of diverse populations of neurons and glia. Single cell gene expression studies have mostly focused on characterization of neuronal cell diversity; however, recent studies have revealed substantial diversity of glial cells, particularly astrocytes. To better understand glial cell types and their roles in neurobiology, we built a new suite of adeno-associated viral (AAV)-based genetic tools to enable genetic access to astrocytes and oligodendrocytes.
Read the full summary ↓
These oligodendrocyte and astrocyte enhancer-AAVs were highly specific, showed variable expression levels, and our astrocyte enhancer-AAVs showed multiple distinct expression patterns that reflected the spatial distribution of astrocyte subtypes. To provide the best glial-specific functional tools, several enhancer-AAVs were: optimized for higher expression levels, shown to be functional and specific in rat and macaque, shown to maintain specific activity in epilepsy where traditional promoters changed activity, and used to drive functional transgenes in astrocytes including Cre recombinase and acetylcholine-responsive sensor iAChSnFR. The astrocyte-specific iAChSnFR revealed a clear reward-dependent acetylcholine response in astrocytes of the nucleus accumbens during reinforcement learning. Together, this collection of glial enhancer-AAVs will enable characterization of astrocyte and oligodendrocyte populations and their roles across species, disease states, and behavioral epochs.
This dataset
Open GSE235987 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 GSE235987_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA988135 and SRA study SRP446192. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
14 conditions, mostly with about 38 replicates each
BrainCell_Enhancer-eHGT_386m_MouseID-616738_C… ×45 BrainCell_Enhancer-eHGT_375m_MouseID-614198_C… ×43 BrainCell_Enhancer-ProB12_MouseID-616739_Cell ×40 BrainCell_Enhancer-eHGT_376h_MouseID-614199_C… ×38 BrainCell_Enhancer-eHGT_381h_MouseID-615516_C… ×38 BrainCell_Enhancer-eHGT_374m_MouseID-614201_C… ×37 BrainCell_Enhancer-eHGT_390m_MouseID-616740_C… ×34 BrainCell_Enhancer-eHGT_380h_MouseID-614200_C… ×34 +11 more

Supports a between-group comparison across 395 samples.

How we read this: 14 replicated groups read from the first 400 of 2040 sample titles; they account for 395 of them. 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

+ 2000 more — browse all 2040 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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