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Bone Marrow Microenvironment in Aplastic Anemia: Insights from Nestin/ CXCL12 Immunohistochemistry and RNA-Sequencing

GSE319656 Homo sapiens (human) RNA-seq (gene expression) 28 samples Submitted 2026/04/08 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 28 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
Homo sapiens (human)
Samples
28 samples: 14 × bone marrow; sAA; 1893-A vs 6 × bone marrow; mAA; 1893-A vs 5 × bone marrow; Control; 1893-A vs 3 × technical control replicate; 1893-HCT-15Groups 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
Nestin/CXCL12 immunohistochemistry and RNA sequencing map the bone marrow microenvironment in aplastic anemiaDisease models & mechanisms · 2026
Summary (written by the submitters)
Aplastic anemia (AA) is a rare bone marrow failure syndrome characterized by immune-mediated destruction of hematopoietic stem and progenitor cells (HSPCs). The contribution of the bone marrow microenvironment remains incompletely understood. We analyzed 29 bone marrow biopsies from patients with moderate (mAA), severe (sAA), and very severe AA (vsAA), along with 12 healthy controls and seven subcortical pseudohypocellular samples.
Read the full summary ↓
Immunohistochemistry for nestin and CXCL12 was performed to quantify stromal niches. RNA sequencing was carried out to investigate immune and niche-related gene expression patterns. sAA patients exhibited a significantly increased number of nestin+ niches compared to mAA and controls. CXCL12+ niches showed no significant differences between groups. RNA sequencing revealed upregulation of immune response genes, as well as pathways related to interferon-gamma signaling, JAK-STAT3 activation, and antigen presentation. Downregulated genes and pathways pointed to impaired DNA repair, cell cycle regulation, and epigenetic stability. Our findings supports a model in which AA pathogenesis is driven by both immune injury and compensatory, yet dysfunctional, stromal remodeling. These data underline the importance of the bone marrow microenvironment in AA.
Published in
Nestin/CXCL12 immunohistochemistry and RNA sequencing map the bone marrow microenvironment in aplastic anemia
Beerlage A, Zinner CP, Passweg JR et al. · Disease models & mechanisms 2026 · PMID 41943582 · doi:10.1242/dmm.052564
This dataset
Open GSE319656 in finder → Find more human 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 GSE319656_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 PRJNA1424923 and SRA study SRP677680. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41943582) ↗
Study design
14 × bone marrow; sAA; 1893-A vs 6 × bone marrow; mAA; 1893-A vs 5 × bone marrow; Control; 1893-A vs 3 × technical control replicate; 1893-HCT-15

Supports a between-group comparison across 28 samples.

How we read this: 4 replicated groups read from 28 sample titles; they account for 28 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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