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ComBO: A combined human bone and lympho-myeloid bone marrow organoid for pre-clinical modelling of haematopoietic disorders

GSE287648 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2026/01/12 Platform GPL24676Platform GPL34284
At a glance

Single-cell RNA-seq · human · 12 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
12 samples: 4 × comBO_d20 bulk gel_biol vs 3 × comBO_d35 granular gel_MM vs 2 × comBO_d35 bulk gel_biol vs 2 × comBO_d35 granular gel_biolGroups 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
comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disordersCell stem cell · 2026
Summary (written by the submitters)
We developed a new combined human bone and lympho-myeloid bone marrow organoid (comBO) model using human induced pluripotent stem cells (hiPSCs). To characterise this model, we employed 10x single-cell RNA sequencing (scRNA-seq) to analyze cell composition and cell-cell interactions. Additionally, we engrafted the comBOs with cells derived from healthy donors or multiple myeloma patients and performed scRNA-seq to explore its potential for disease modeling.
Published in
comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders
Shen Y, Benlabiod C, Watson E et al. · Cell stem cell 2026 · PMID 41734765 · doi:10.1016/j.stem.2026.01.010
This dataset
Open GSE287648 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 GSE287648_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 PRJNA1214192 and SRA study SRP559044. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41734765) ↗
Study design
4 × comBO_d20 bulk gel_biol vs 3 × comBO_d35 granular gel_MM vs 2 × comBO_d35 bulk gel_biol vs 2 × comBO_d35 granular gel_biol

Supports a between-group comparison across 11 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 11 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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