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RNA profiles of hematopoietic stem cells before and after long-term culture [RNA-Seq]

GSE338821 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2026/07/17 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 5 conditions, mostly with about 4 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.
Summary (written by the submitters)
Self-renewing hematopoietic stem cells (HSCs) during hematopoietic regeneration showed lower intracellular glutamate (Glu) levels compared with dividing progenitor cells in the steady state and HSCs attenuate stem cell function during ex vivo culture. R162, an inhibitor of glutamine dehydrogenase (Glud1) that catabolize Glu into α-ketoglutarate, contributed to stem cell maintenance during ex vivo culture. These data suggest that lower intracellular Glu levels during HSC division contributed to self-renewing divisions by suppressing Glud1-mediated reactions.
This dataset
Open GSE338821 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 GSE338821_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 PRJNA1496069 and SRA study SRP718481. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 conditions, mostly with about 4 replicates each
30-day_cultured_EPCR_High_HSC ×8 Uncultured_EPCR_High_HSC ×4 Uncultured_EPCR_Low_HSC ×4 5-day_cultured_EPCR_High_HSC ×4 5-day_cultured_EPCR_Low_HSC ×4

Supports a between-group comparison across 24 samples.

How we read this: 5 replicated groups read from 24 sample titles; they account for 24 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
Datasets on a similar topic

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