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Single cell RNA sequencing of bone marrow cells in patients post allogenic stem cell transplantation

GSE293012 Homo sapiens (human) Single-cell RNA-seq 33 samples Submitted 2026/03/16 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 33 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Samples
33 samples: 11 × PGF-BCR_S vs 11 × PGF-TCR_S vs 10 × PGF-GEX1_SGroups 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
T cell and monocyte activation in concert with hematopoietic stem cell interactions shapes the post-allogeneic transplant immune landscape in poor graft functionFrontiers in immunology · 2026
Summary (written by the submitters)
We performed single cell RNA sequencing, and VDJ sequencing of TCR and BCR of bone marrow samples (BMMMNCs) from 11 patients who received allogenic stem cell transplantation, among them, 5 with good graft function and 6 with poor graft function, to understand hematopoietic and immune reconstitution after stem cell transplantation, and potential mechanisms of poor graft function.
Published in
T cell and monocyte activation in concert with hematopoietic stem cell interactions shapes the post-allogeneic transplant immune landscape in poor graft function
Prabahran A, Wu Z, Gao S et al. · Frontiers in immunology 2026 · PMID 41716418 · doi:10.3389/fimmu.2026.1750093
This dataset
Open GSE293012 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 GSE293012_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1242348 and SRA study SRP573375. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41716418) ↗
Study design
11 × PGF-BCR_S vs 11 × PGF-TCR_S vs 10 × PGF-GEX1_S

Supports a between-group comparison across 32 samples.

How we read this: 3 replicated groups read from 33 sample titles; they account for 32 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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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.