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mRNA 3ʹ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth dataset 6

GSE318678 Mus musculus (mouse) RNA-seq (gene expression) 48 samples Submitted 2026/04/08 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 48 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
48 samples: 12 conditions, mostly with about 4 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
mRNA 3' UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growthGenes & development · 2026
Summary (written by the submitters)
MicroRNAs direct downregulation of target mRNAs. Sometimes, however, this regulatory paradigm inverts, and a target RNA triggers degradation of a microRNA. This target-directed microRNA degradation (TDMD) requires ZSWIM8. Zswim8-/- mice exhibit reduced growth and perinatal lethality, accompanied by stabilization of >40 microRNAs. Nonetheless, studies of TDMD function in mammals have been limited because only two TDMD-triggering RNAs have been identified in mice.
Read the full summary ↓
Here, we computationally identify and validate five new TDMD-triggering sites in mouse models. One site in Atp6v1g1 and two in Lpar4 direct degradation of miR-335-3p, showing that in mammals, two sites in the same transcript, and multiple sites in different transcripts, can collaborate to destabilize a microRNA. Moreover, sites in Plagl1 and Lrrc58 direct degradation of miR-322 and miR-503, respectively. Mice lacking the Plagl1 and Lrrc58 sites were smaller, demonstrating that target-directed degradation of miR-322 and miR-503 promotes growth. Both miR-335-3p and Plagl1 are maternally imprinted, implying their participation in parental conflict, but their corresponding triggers or target microRNA partner are not imprinted. Thus, 3¢ UTRs can participate in parental conflict not only by regulating protein production but also directly by engaging TDMD to access an additional layer of regulation within a network of imprinted and biallelic genes.
Published in
mRNA 3' UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth
Lin DH, Elcavage LE, Khalizeva E et al. · Genes & development 2026 · PMID 41871909 · doi:10.1101/gad.353479.125
This dataset
Open GSE318678 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 GSE318678_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 PRJNA1419769 and SRA study SRP675213. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41871909) ↗
Study design
12 conditions, mostly with about 4 replicates each
mRNA E18.5 stomach Plagl1 WT pup ×4 mRNA E18.5 stomach Plagl1 mut(pat) pup ×4 mRNA E18.5 lung Lrrc58 WT pup ×4 mRNA E18.5 lung Lrrc58 hom pup ×4 mRNA E18.5 heart Atp6v1g1 WT pup ×4 mRNA E18.5 heart Atp6v1g1 hom pup ×4 mRNA E18.5 lung Atp6v1g1 WT pup ×4 mRNA E18.5 lung Atp6v1g1 hom pup ×4 +4 more

Supports a between-group comparison across 48 samples.

How we read this: 12 replicated groups read from 48 sample titles; they account for 48 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

+ 8 more — browse all 48 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.