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Ileal Enterocyte Brush Border Abnormalities Associate with Progressive Disease Course in Pediatric Crohn’s Disease

GSE264073 Homo sapiens (human) RNA-seq (gene expression) 152 samples Submitted 2025/12/17 Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 152 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
152 samples: 138 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
Short Ileal Microvillus Length Phenotype Associates with Progression from Inflammatory to Complicated Disease Behavior in Pediatric Crohn's DiseaseInflammatory bowel diseases · 2026
Summary (written by the submitters)
Objective: There is a critical need for biomarkers to predict prognosis and guide clinical care in pediatric Crohn’s disease (CD). Our previous studies of adult CD indicated ileal microvillus length as a potential prognostic biomarker for therapy response. Here, we tested if short microvillus length predicted progression of disease behavior or bowel resection surgery in pediatric CD.
Read the full summary ↓
Design: We obtained H&E-stained ileal histology samples from 3 pediatric CD cohorts. Average microvillus length was determined for 59 Control and 377 CD samples and tested for associations with patient demographic and clinical data, RNA-seq molecular profiles, histological inflammation scores, and clinical outcomes. Results: Relative to Controls, the average microvillus length was shorter in CD samples collected at diagnostic or follow-up colonoscopy procedures. Microvillus length was generally not associated with demographic data or clinical activity indices. The CD molecular signature was functionally enriched for transporter activity and brush border membrane among the genes positively associated with microvillus length and for extracellular matrix, inflamed macrophages, and fibroblasts among the genes negatively associated with microvillus length. Microvillus length negatively correlated with histologic inflammation score, but short microvillus length phenotype could cooccur with low histologic inflammation. There was a higher likelihood of stricturing disease behavior or bowel resection surgery, but not fistulizing disease behavior, in follow-up CD samples with short microvillus length. Conclusion: Short microvillus length can predict the development of stricturing disease behavior and bowel resection surgery in pediatric CD, further supporting the potential use of this histological phenotype as a biomarker for CD prognosis.
Published in
Short Ileal Microvillus Length Phenotype Associates with Progression from Inflammatory to Complicated Disease Behavior in Pediatric Crohn's Disease
Haberman Y, Braun T, Karns R et al. · Inflammatory bowel diseases 2026 · PMID 41309136 · doi:10.1093/ibd/izaf288
This dataset
Open GSE264073 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 GSE264073_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 PRJNA1100929 and SRA study SRP502014. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41309136) ↗
Study design
138 distinct titles, 1 of them repeated
RK ×15

How we read this: Read from 152 sample titles: 138 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

+ 112 more — browse all 152 samples with per-sample file links →

Datasets on a similar topic

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