GEO series

Technical and biological sources of noise confound multiplexed enhancer AAV screening [dataset2]

GSE311154 Mus musculus (mouse) Single-cell RNA-seq 904 samples Submitted 2026/02/23 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 904 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: 904 samples
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

Summary (written by the submitters)

Cis-acting regulatory enhancer elements are valuable tools for gaining cell type-specific genetic access. Leveraging large chromatin accessibility atlases, putative enhancer sequences can be identified and deployed in adeno-associated virus (AAV) delivery platforms. However, a significant bottleneck in enhancer AAV discovery is charting their detailed expression patterns in vivo, a process that currently requires gold-standard one-by-one testing.

Read the full summary ↓

Here we perform barcoded multiplexed screening of enhancer AAVs at cell type resolution using single cell RNA sequencing and taxonomy mapping. We executed a proof-of-concept study using small pools of well-validated enhancer-AAVs expressing in a variety of neuronal and non-neuronal cell types across the mouse brain. Unexpectedly, we encountered substantial technical and biological noise including chimeric packaging products, necessitating development of novel techniques to accurately deconvolve enhancer expression patterns. These results underscore the need for improved methods to mitigate noise and highlight the complexity of enhancer AAV biology in vivo.

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 GSE311154 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 GSE311154_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 PRJNA1368752 and SRA study SRP651119. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42049725) ↗

Samples in this study

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+ 904 more — browse all 904 samples with per-sample file links →

Datasets on a similar topic

GSE311152 Technical and biological sources of noise confound multiplexed enhancer AAV screening [dataset1] 800 samples shares aav, multiplexed, biological, technical, screening, confound, enhancer
GSE311156 Technical and biological sources of noise confound multiplexed enhancer AAV screening [dataset3] 797 samples shares aav, multiplexed, biological, technical, screening, confound, enhancer
GSE312364 Technical and biological sources of noise confound multiplexed enhancer AAV screening 2548 samples shares aav, multiplexed, biological, technical, screening, confound, enhancer
GSE312361 Technical and biological sources of noise confound multiplexed enhancer AAV screening [dataset4] 47 samples shares aav, multiplexed, biological, technical, screening, confound, enhancer
GSE235987 Enhancer-AAVs allow genetic access to diverse populations of astrocytes and oligodendrocytes across species 2040 samples shares aav, enhancer
GSE304349 The regulatory code of injury responsive enhancers enables precision cell state targeting in the CNS [enhancer_aav] 4 samples shares aav, enhancer
GSE57597 Genotoxicity after adeno-associated virus (AAV) gene therapy is dependent upon dose, treatment age and enhancer-promoter selection 58 samples shares aav, enhancer
GSE298405 In vivo screening for essential metabolic mediators in mouse model of lung inflammation using AAV9-ME CRISPR library 8 samples shares aav, screening

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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.