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Technical and biological sources of noise confound multiplexed enhancer AAV screening

GSE312364 Mus musculus (mouse) RNA-seq (gene expression) 2548 samples Submitted 2026/02/18 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 2548 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
2548 samples: 19 conditions, mostly with about 8 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.
Paper
Technical and biological sources of noise confound multiplexed enhancer AAV screeningNature communications · 2026
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Technical and biological sources of noise confound multiplexed enhancer AAV screening
Hunker AC, Mich JK, Taskin N et al. · Nature communications 2026 · PMID 42049725 · doi:10.1038/s41467-026-72147-8
This dataset
Open GSE312364 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 GSE312364_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 PRJNA1373169 and SRA study SRP648049. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42049725) ↗
Study design
19 conditions, mostly with about 8 replicates each
C57Bl/6 YFP+ ALM single nucleus hSyn1-H2B-SYF… ×40 C57Bl/6 YFP+ ALM single nucleus AiE0390m-H2B-… ×40 C57Bl/6 YFP+ ALM single nucleus AiE0410m-H2B-… ×40 C57Bl/6 YFP+ ALM single nucleus CMV-H2B-SYFP2… ×40 C57Bl/6 YFP+ ALM single nucleus DLX2.0-H2B-SY… ×40 C57Bl/6 YFP+ ALM single nucleus AiE0387m-H2B-… ×24 C57Bl/6 YFP+ ALM single nucleus AiE0401h-H2B-… ×24 C57Bl/6 YFP+ ALM single nucleus AiE0391h-H2B-… ×24 +11 more

Supports a between-group comparison across 400 samples.

How we read this: 19 replicated groups read from the first 400 of 2548 sample titles; they account for 400 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

+ 2508 more — browse all 2548 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.