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Ftsj1 deficiency influences diverse ncRNA networks in murine organs (poly-A-seq and rRNA-depletion-seq)

GSE285757 Mus musculus (mouse) RNA-seq (gene expression) 60 samples Submitted 2026/03/17 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 60 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
60 samples: 20 conditions, mostly in triplicateGroups 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
Cross-organ communication based on non-coding RNA networks leads to cognitive dysfunction in miceNeurobiology of disease · 2026
Summary (written by the submitters)
Beyond the regulation of mRNAs by individual ncRNA types, such as miRNAs or lncRNAs, their interplay as so-called competitive endogenous RNAs (ceRNAs) appears to play a pivotal role in diseases. In our study we aimed to get a holistic understanding of the tRNA 2’O-methyltransferase FTSJ1 and its regulatory role in the context of cognitive disability.
Read the full summary ↓
Here, we investigated the impact of Ftsj1 deficiency on ceRNA networks across different mouse organs. Our study underscores the critical role of organ-specific ceRNA networks, particularly in metabolic regulation, and emphasizes the need for cross-organ analyses to unravel the complexity of ceRNA-mediated gene regulation. Our findings reveal a prominent ceRNA network in the liver, mediated by four hub miRNAs (miR-378d, miR-3076-5p, miR-3474, and miR-296-3p) and enriched with acetyl CoA-related genes, including Acly, Acss2, and Mvk. These genes are integral to fatty acid metabolism, which is heavily disrupted in both liver and kidney. In contrast, brain tissues exhibited minimal changes, suggesting only a limited impact directly related to Ftsj1 in this organ. These results suggest that the cognitive disability associated with Ftsj1 is driven by metabolic and ceRNA crosstalk along the liver-brain and kidney-brain axes. This dataset comprises the poly-A and rRNA-depletion total RNA sequencing data used in our study for mRNAs and lncRNAs.
Published in
Cross-organ communication based on non-coding RNA networks leads to cognitive dysfunction in mice
Dunkel H, Jensen LR, Sperling F et al. · Neurobiology of disease 2026 · PMID 41692170 · doi:10.1016/j.nbd.2026.107319
This dataset
Open GSE285757 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 GSE285757_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 PRJNA1205766 and SRA study SRP555008. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41692170) ↗
Study design
20 conditions, mostly in triplicate
mouse poly-A seq Brain Ftsj1_DF ×3 mouse poly-A seq Brain WT ×3 mouse poly-A seq Heart Ftsj1_DF ×3 mouse poly-A seq Heart WT ×3 mouse poly-A seq Kidney Ftsj1_DF ×3 mouse poly-A seq Kidney WT ×3 mouse poly-A seq Liver Ftsj1_DF ×3 mouse poly-A seq Liver WT ×3 +12 more

Supports a between-group comparison across 60 samples.

How we read this: 20 replicated groups read from 60 sample titles; they account for 60 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

+ 20 more — browse all 60 samples with per-sample file links →

Datasets on a similar topic

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