GEO series

GABA produced by multiple bone marrow niche cell types regulate hematopoietic stem and progenitor cells

GSE294951 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2025/10/16 Platform GPL34290

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: 3 × Cd19 vs 3 × Tie2 vs 3 × WT vs 3 × cdh5Groups 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: GABA produced by multiple bone marrow cell types regulates hematopoietic stem and progenitor cellsStem cell reports · 2025

Summary (written by the submitters)

Hematopoietic stem and progenitor cells (HSPCs) maintain homeostasis of the blood system by balancing proliferation and differentiation. Many extrinsic signals in the bone marrow (BM) microenvironment that regulate this balance are still unknown. We report gamma aminobutyric acid (GABA) metabolite produced in the BM as a regulator of HSPCs .

Read the full summary ↓

Deletion of the glutamate decarboxylase enzymes (Gad1/2) that produce GABA in either B lineages or BM endothelial cells (BMECs) leads to a moderate reduction in BM GABA levels and HSPC number, suggesting both cell types are GABA sources. However, simultaneous blockade of GABA production from both hematopoietic cells and BMECs resulted in a greater reduction of both GABA levels and HSPC numbers. Lower GABA levels in the BM altered the gene expression profile of HSPCs, with expression reduced for proliferation-associated genes and increased for B lineage genes . Our findings suggest GABA from multiple sources coordinates to regulate HSPC activity.

Published in

GABA produced by multiple bone marrow cell types regulates hematopoietic stem and progenitor cells

Deng C, Elujoba-Bridenstine A, Song AT et al. · Stem cell reports 2025 · PMID 41106387 · doi:10.1016/j.stemcr.2025.102677

This dataset

Open GSE294951 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 GSE294951_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 PRJNA1252090 and SRA study SRP579459. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41106387) ↗

Study design

3 × Cd19 vs 3 × Tie2 vs 3 × WT vs 3 × cdh5

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM8931928 Cd19-1 Cd19
GSM8931929 Cd19-2 Cd19
GSM8931930 Cd19-3 Cd19
GSM8931931 Tie2-1 Tie2
GSM8931932 Tie2-2 Tie2
GSM8931933 Tie2-3 Tie2
GSM8931934 WT-1 WT
GSM8931935 WT-2 WT
GSM8931936 WT-3 WT
GSM8931937 cdh5-1 cdh5
GSM8931938 cdh5-2 cdh5
GSM8931939 cdh5-3 cdh5

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