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Single cell transcription profiles of hematopoietic stem and progenitor cells from Beta thalassemia transfusion dependent patients in steady state condition

GSE263204 Homo sapiens (human) Single-cell RNA-seq 10 samples Submitted 2025/04/11 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 10 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
10 samples: 9 distinct titles, 1 of them repeatedGroups 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
Imbalanced TGFβ signalling and autophagy drive erythroid priming of hematopoietic stem cells in β-thalassemiaNature communications · 2025
Summary (written by the submitters)
We investigated the composition of the hematopoietic stem and progenitor pool in beta-thalassemia (BThal) patients by perfoming scRNA-seq on CD34+ hematopoietic stem progenitor cells (HSPCs) and on single phenotypic hematopoietic stem/multiputent cells (HSCs/MPPs). These single-cell approaches reveal molecular and functional heterogeneity within the HSPC compartment in the bone marrow from Bthal patients in steady state condition in comparison with aged matched pediatric patients.
Published in
Imbalanced TGFβ signalling and autophagy drive erythroid priming of hematopoietic stem cells in β-thalassemia
Lidonnici MR, Chianella G, Mende N et al. · Nature communications 2025 · PMID 40592819 · doi:10.1038/s41467-025-60676-7
This dataset
Open GSE263204 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 GSE263204_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 PRJNA1096269 and SRA study SRP499741. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40592819) ↗
Study design
9 distinct titles, 1 of them repeated
B60166112019 CD34 ×2

How we read this: Read from 10 sample titles: 9 distinct titles with little repetition. 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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