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Transcriptomics of mouse bone marrow erythropoiesis

GSE226078 Mus musculus (mouse) RNA-seq (gene expression) 68 samples Submitted 2024/11/15 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 68 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
68 samples: 18 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
A glutamine metabolic switch supports erythropoiesisScience (New York, N.Y.) · 2024
Summary (written by the submitters)
Metabolic requirements vary during tissue development, but little is known whether and how metabolic rewiring orchestrates lineage differentiation and maturation. We discovered an essential metabolic switch from glutamine catabolism to glutamine synthesis during erythropoiesis. Glutamine synthetase (GS), one of the oldest functioning genes, is induced during terminal maturation to promote detoxification of ammonia generated during heme biosynthesis, which is massively upregulated to support hemoglobin production.
Read the full summary ↓
Loss of GS in mouse erythroid precursors causes ammonia accumulation, oxidative stress, leading to maturation arrest and apoptosis. In β-thalassemia, GS activity is impaired by protein oxidation, causing glutamate and ammonia accumulation, whereas enforced GS expression alleviates the metabolic and pathologic defects. These results identify an evolutionarily conserved metabolic adaptation that may be leveraged to treat common red cell disorders.
Published in
A glutamine metabolic switch supports erythropoiesis
Lyu J, Gu Z, Zhang Y et al. · Science (New York, N.Y.) 2024 · PMID 39541460 · doi:10.1126/science.adh9215
This dataset
Open GSE226078 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 GSE226078_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 PRJNA938477 and SRA study SRP424499. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39541460) ↗
Study design
18 conditions, mostly in triplicate
BM_ERY-I ×7 BM_ERY-V ×7 BM_CFU-E ×5 BM_ERY-II ×4 BM_ERY-III ×4 BM_ERY-IV ×4 BM_ERY-VI ×4 BM_BFU-E ×3 +10 more

Supports a between-group comparison across 68 samples.

How we read this: 18 replicated groups read from 68 sample titles; they account for 68 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

+ 28 more — browse all 68 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.