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Systems genetics reveals the influence of eQTLs in mouse embryonic stem cells on transcriptional variation later in differentiated neural progenitor cells

GSE285231 Mus musculus (mouse) RNA-seq (gene expression) 186 samples Submitted 2025/01/24 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 186 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
186 samples: 13 conditions, mostly with about 10 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
Systems genetics reveals the influence of expression QTLs in mouse embryonic stem cells on transcriptional variation later in differentiated neural progenitor cellsG3 (Bethesda, Md.) · 2025
Summary (written by the submitters)
Genetic variation leads to phenotypic variability in pluripotent stem cells that presents challenges for regenerative medicine. Although recent studies have investigated the impact of genetic variation on pluripotency maintenance and differentiation capacity, less is known about how genetic variants affecting the pluripotent state influence gene regulation later in development.
Read the full summary ↓
Here, we characterized expression of 12,000 genes in a large panel of donor-matched Diversity Outbred (DO) mouse embryonic stem cell (mESC) and neural progenitor cell (mNPC) lines. Quantitative trait locus (QTL) mapping identified 4,060 expression QTL (eQTL) in mNPCs, including 2,998 local and 1,062 distant eQTL. In a comparison of mNPC and mESC eQTLs, we found that local eQTLs were more likely than distant eQTL to be detected in both cell types. Distant eQTL were largely unique to one cell type, and we mapped three mNPC-specific eQTL hotspots on Chromosomes (Chrs) 1, 10, and 11. Mediation analysis of the Chr 1 hotspot identified Rnf152 as the best candidate mediator expressed in mNPCs, while cross-cell type mediation using mESC gene expression along with partial correlation analysis strongly implicated genetic variant(s) affecting Pign expression in the mESC state as regulating the mNPC Chr 1 hotspot. These findings highlight that local mNPC eQTL are more likely than distant eQTL to be shared with mESCs; distant mNPC eQTL are numerous but largely unique to that cell type, with many co-localizing to mNPC-specific hotspots; and mediation analysis across cell types suggests that expression of Pign in mESCs shapes the transcriptome of the more specialized mNPC state.
Published in
Systems genetics reveals the influence of expression QTLs in mouse embryonic stem cells on transcriptional variation later in differentiated neural progenitor cells
Aydin S, Skelly DA, Dewey HB et al. · G3 (Bethesda, Md.) 2025 · PMID 40327589 · doi:10.1093/g3journal/jkaf099
This dataset
Open GSE285231 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 GSE285231_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 PRJNA1202081 and SRA study SRP553369. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40327589) ↗
Study design
13 conditions, mostly with about 10 replicates each
DO mNPC Sample PB360 ×37 DO mNPC Sample PB361 ×28 DO mNPC Sample PB359 ×23 DO mNPC Sample PB358 ×21 DO mNPC Sample PB362 ×11 DO mNPC Sample PB366 ×10 DO mNPC Sample PB367 ×10 DO mNPC Sample PB368 ×10 +7 more

Supports a between-group comparison across 184 samples.

How we read this: 13 replicated groups read from 186 sample titles; they account for 184 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

+ 146 more — browse all 186 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.