GEO series

The reparative immunologic consequences of stem cell transplantation as a cellular therapy for refractory Crohn’s disease

GSE284677 Homo sapiens (human) Single-cell RNA-seq 36 samples Submitted 2025/01/23 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 36 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: 36 samples: 36 samples, each with a distinct title — no replicated groupsGroups 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: Reparative immunological consequences of stem cell transplantation as a cellular therapy for refractory Crohn's diseaseGut · 2025

Summary (written by the submitters)

Background Treatment strategies for Crohn’s disease (CD) suppress diverse inflammatory pathways but many patients remain refractory to treatment. Autologous hematopoietic stem cell transplantation (SCT) is an emerging therapy for medically-refractory CD though the mechanisms through which it circumvents refractory pathophysiology are unknown.

Read the full summary ↓

Objective The objective of this study is to understand how the immune system reconstitutes post-SCT and whether SCT may function as a cellular therapy restoring appropriately responsive immune cell populations from hematopoietic stem cells (HSCs). Design Adults with CD with active clinical and endoscopic disease who failed available medical therapies were enrolled in a Phase II study of SCT for refractory CD (n=19). Blood and intestinal samples were collected longitudinally and analyzed using CyTOF, scRNA-seq and TCRβ-seq. Stem cell autografts were functionally assayed in mouse xenograft models. Results scRNA-seq and CyTOF analyses reveal that SCT predominantly affected the intestinal myeloid lineage with loss of inflammatory populations and return of macrophages capable of supporting mucosal healing. Xenograft models using patient HSCs suggested HSCs support the early reconstitution of the myeloid lineage and reveal an impairment of short and long-term HSC engraftment that may determine SCT outcomes. Conclusions This study suggests SCT functions as a myeloid-directed cellular therapy reinforcing the critical role of macrophages in refractory CD pathophysiology and as a target for cellular therapies. Furthermore, we report an unrecognized functional heterogeneity among HSC subpopulations in CD that may be relevant to our understanding of CD treatment and pathophysiology.

Published in

Reparative immunological consequences of stem cell transplantation as a cellular therapy for refractory Crohn's disease

Guisado D, Talware S, Wang X et al. · Gut 2025 · PMID 39961646 · doi:10.1136/gutjnl-2024-333558

This dataset

Open GSE284677 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 GSE284677_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 PRJNA1200031 and SRA study SRP552438. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39961646) ↗

Study design

36 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 36 sample titles: 36 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

GSM8690416 PT18 ileum baseline
GSM8690417 PT15 ileum baseline
GSM8690418 PT15 jejunum baseline
GSM8690419 PT13 ileum 6 months post-SCT
GSM8690420 PT12 jejunum 6 months post-SCT
GSM8690421 PT12 ileum 6 months post-SCT
GSM8690422 PT14 ileum baseline
GSM8690423 PT16 ileum baseline
GSM8690424 PT19 ileum baseline
GSM8690425 PT11 ileum 6 months post-SCT
GSM8690426 PT13 ileum baseline
GSM8690427 PT17 blood baseline
GSM8690428 PT13 blood 3 months post-SCT
GSM8690429 PT15 blood baseline
GSM8690430 PT18 blood stem cell collection
GSM8690431 PT13 blood engraftment
GSM8690432 PT18 blood stem cell graft
GSM8690433 PT18 blood stem cell graft CD34+ selected
GSM8690434 PT11 blood 12 months post-SCT
GSM8690435 PT18 blood engraftment
GSM8690436 PT13 blood 6 months post-SCT
GSM8690437 PT12 blood 6 months post-SCT
GSM8690438 PT19 blood stem cell graft
GSM8690439 PT14 blood baseline
GSM8690440 PT12 blood engraftment
GSM8690441 PT16 blood baseline
GSM8690442 PT18 blood baseline
GSM8690443 PT12 blood baseline
GSM8690444 PT11 blood 6 months post-SCT
GSM8690445 PT13 blood stem cell graft
GSM8690446 PT19 blood stem cell collection
GSM8690447 PT12 blood stem cell graft
GSM8690448 PT11 blood stem cell collection
GSM8690449 PT11 blood engraftment
GSM8690450 PT11 blood 3 months post-SCT
GSM8690451 PT13 blood baseline

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