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Combination of Cas9 and adeno-associated vectors (AAVs) enables efficient in vivo knockdown of precise miRNAs in the rodent brain

GSE291994 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2025/03/19 Platform GPL19057

At a glance

RNA-seq (gene expression) · mouse · 28 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: 28 samples: 28 samples, each with a distinct title — no replicated groupsGroups 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: Combination of Cas9 and adeno-associated vectors enables efficient in vivo knockdown of precise miRNAs in the rodent and primate brainProceedings of the National Academy of Sciences of the United States of America · 2025

Summary (written by the submitters)

Although the advent of Cas9 technology has expanded our ability to precisely edit the genome, manipulating microRNAs in vivo has been shown to be particularly challenging, especially in the brain. Here, we sought to generate novel tools aiming at targeting and efficiently downregulating defined microRNAs species in a cell-specific manner so that their function in discrete neuronal networks could be investigated.

Read the full summary ↓

Focusing on miR-124, a microRNA highly expressed in the mammalian brain and transcribed from three independent chromosomal loci, we designed and validated different gRNAs directed against this miRNA. In vitro, our Cas9 designs show not only a significant reduction in miR-124 levels but also a functional effect on miR-124 silencing. Similarly, when packed into AAV vectors and injected into the mouse cortex, miR-124-Cas9 vectors strongly downregulate miR-124 levels without affecting the expression of other miRNAs. In parallel, levels of endogenous miR-124 targets exhibit a significant increase supporting the release of its silencing activity. To functionally validate our tools, we provide evidences that deletion of miR-124 in the subventricular zone altered migration of newly generated neurons into the olfactory bulb. Finally, we also showed that our vectors altered the expression of Gria 2, a canonical target of miR-124, and modified the Ca2+ permeability of AMPA receptors. These tools are expected to help elucidating miRNA function in complex experimental settings such as brain networks in vivo.

Published in

Combination of Cas9 and adeno-associated vectors enables efficient in vivo knockdown of precise miRNAs in the rodent and primate brain

Roura-Martinez D, Popa N, Jaouen F et al. · Proceedings of the National Academy of Sciences of the United States of America 2025 · PMID 41359835 · doi:10.1073/pnas.2513076122

This dataset

Open GSE291994 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 GSE291994_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 PRJNA1236301 and SRA study SRP570471. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41359835) ↗

Study design

28 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 28 sample titles: 28 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

GSM8846245 Mouse 17, AAV-Cas9-miR-124-empty, Cas9 positive nuclei
GSM8846246 Mouse 18, AAV-Cas9-miR-124-empty, Cas9 positive nuclei
GSM8846247 Mouse 19, AAV-Cas9-miR-124-empty, Cas9 positive nuclei
GSM8846248 Mouse 20, AAV-Cas9-miR-124-empty, Cas9 positive nuclei
GSM8846249 Mouse 21, AAV-Cas9-miR-124-empty, Cas9 positive nuclei
GSM8846250 Mouse 22, AAV-Cas9-miR-124-empty, Cas9 positive nuclei
GSM8846251 Mouse 23, AAV-Cas9-miR-124-empty, Cas9 positive nuclei
GSM8846252 Mouse 17, AAV-Cas9-miR-124-g4, Cas9 positive nuclei
GSM8846253 Mouse 18, AAV-Cas9-miR-124-g4, Cas9 positive nuclei
GSM8846254 Mouse 19, AAV-Cas9-miR-124-g4, Cas9 positive nuclei
GSM8846255 Mouse 20, AAV-Cas9-miR-124-g4, Cas9 positive nuclei
GSM8846256 Mouse 21, AAV-Cas9-miR-124-g4, Cas9 positive nuclei
GSM8846257 Mouse 22, AAV-Cas9-miR-124-g4, Cas9 positive nuclei
GSM8846258 Mouse 23, AAV-Cas9-miR-124-g4, Cas9 positive nuclei
GSM8846259 Mouse 17, AAV-Cas9-miR-124-empty, Cas9 negative nuclei
GSM8846260 Mouse 18, AAV-Cas9-miR-124-empty, Cas9 negative nuclei
GSM8846261 Mouse 19, AAV-Cas9-miR-124-empty, Cas9 negative nuclei
GSM8846262 Mouse 20, AAV-Cas9-miR-124-empty, Cas9 negative nuclei
GSM8846263 Mouse 21, AAV-Cas9-miR-124-empty, Cas9 negative nuclei
GSM8846264 Mouse 22, AAV-Cas9-miR-124-empty, Cas9 negative nuclei
GSM8846265 Mouse 23, AAV-Cas9-miR-124-empty, Cas9 negative nuclei
GSM8846266 Mouse 17, AAV-Cas9-miR-124-g4, Cas9 negative nuclei
GSM8846267 Mouse 18, AAV-Cas9-miR-124-g4, Cas9 negative nuclei
GSM8846268 Mouse 19, AAV-Cas9-miR-124-g4, Cas9 negative nuclei
GSM8846269 Mouse 20, AAV-Cas9-miR-124-g4, Cas9 negative nuclei
GSM8846270 Mouse 21, AAV-Cas9-miR-124-g4, Cas9 negative nuclei
GSM8846271 Mouse 22, AAV-Cas9-miR-124-g4, Cas9 negative nuclei
GSM8846272 Mouse 23, AAV-Cas9-miR-124-g4, Cas9 negative nuclei

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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.