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Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from adult WT and Dp16 mouse liver tissue ± high fat diet

GSE296500 Mus musculus (mouse) RNA-seq (gene expression) 45 samples Submitted 2025/11/25 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 45 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
45 samples: 13 conditions, mostly in duplicateGroups 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
Altered hepatic metabolism in Down syndromeCell reports · 2026
Summary (written by the submitters)
Analysis of steady-state mRNA levels in mouse liver tissue at 13-15 weeks from wild-type C57BL/6J and Dp(16)1Yey mice fed control or high fat diet.
Published in
Altered hepatic metabolism in Down syndrome
Dunn LN, Niemeyer BF, Eduthan NP et al. · Cell reports 2026 · PMID 41538324 · doi:10.1016/j.celrep.2025.116835
This dataset
Open GSE296500 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 GSE296500_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 PRJNA1259507 and SRA study SRP583419. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41538324) ↗
Study design
13 conditions, mostly in duplicate
Wild-type C57BL/6J; Control diet; Sample_T3 ×5 Wild-type C57BL/6J; High fat diet; Sample_T0 ×3 Dp16; High fat diet; Sample_T1 ×3 Wild-type C57BL/6J; High fat diet; Sample_T2 ×2 Wild-type C57BL/6J; High fat diet; Sample_T6 ×2 Wild-type C57BL/6J; High fat diet; Sample_T4 ×2 Wild-type C57BL/6J; High fat diet; Sample_T5 ×2 Dp16; Control diet; Sample_T4 ×2 +19 more

Supports a between-group comparison across 31 samples.

How we read this: 13 replicated groups read from 45 sample titles; they account for 31 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

+ 5 more — browse all 45 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.