GEO series

RNA-seq of activated murine CD8+ T-cells cultured in high (0.625 mg/mL holotransferrin) or low iron (0.001 mg/mL holotransferrin) conditions with or without 40 mM aspartate

GSE251963 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/03/22 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 12 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: 12 samples: 12 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: Iron deficiency causes aspartate-sensitive dysfunction in CD8(+) T cellsNature communications · 2025

Summary (written by the submitters)

Iron is an irreplaceable co-factor for metabolism and iron deficiency affects >1 billion people, causing anaemia and impairing immunity. How iron deprivation influences normal cellular function remains poorly characterised. In activated CD8+ T-cells we found that iron scarcity profoundly stalled proliferation and disrupted mitochondrial redox control without influencing cell viability.

Read the full summary ↓

The TCA cycle was partially redirected to a reductive trajectory, and the repressive H3K27me3 histone mark, usually decreased post-activation, was maintained. Surprisingly, aspartate, which is crucial for proliferation, was increased in stalled iron deficient cells but was not utilised cytosolically, indicating trapping within depolarised mitochondria. Exogenous aspartate increased ATP, suppressed H3K27me3 and markedly rescued clonal expansion. We propose that iron scarcity creates a metabolic bottleneck impairing activation and proliferation of T-cells, and which is bypassed by resupplying biochemical processes with aspartate. These findings reveal mechanistic consequences of iron deficiency and shed light on the response of T-cells to nutritional variation.

Published in

Iron deficiency causes aspartate-sensitive dysfunction in CD8(+) T cells

Teh MR, Gudgeon N, Frost JN et al. · Nature communications 2025 · PMID 40541943 · doi:10.1038/s41467-025-60204-7

This dataset

Open GSE251963 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 GSE251963_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 PRJNA1056036 and SRA study SRP479751. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40541943) ↗

Study design

12 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 12 sample titles: 12 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

GSM7990633 CD8+ T-cells, mouse 1, 0.625 mg/mL holotransferrin
GSM7990634 CD8+ T-cells, mouse 1, 0.625 mg/mL holotransferrin + 40 mM aspartate
GSM7990635 CD8+ T-cells, mouse 1, 0.001 mg/mL holotransferrin
GSM7990636 CD8+ T-cells, mouse 1, 0.001 mg/mL holotransferrin + 40 mM aspartate
GSM7990637 CD8+ T-cells, mouse 2, 0.625 mg/mL holotransferrin
GSM7990638 CD8+ T-cells, mouse 2, 0.625 mg/mL holotransferrin + 40 mM aspartate
GSM7990639 CD8+ T-cells, mouse 2, 0.001 mg/mL holotransferrin
GSM7990640 CD8+ T-cells, mouse 2, 0.001 mg/mL holotransferrin + 40 mM aspartate
GSM7990641 CD8+ T-cells, mouse 3, 0.625 mg/mL holotransferrin
GSM7990642 CD8+ T-cells, mouse 3, 0.625 mg/mL holotransferrin + 40 mM aspartate
GSM7990643 CD8+ T-cells, mouse 3, 0.001 mg/mL holotransferrin
GSM7990644 CD8+ T-cells, mouse 3, 0.001 mg/mL holotransferrin + 40 mM aspartate

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