A Blood-based Transcriptomic Signature Stratifies Severe Crohn's disease and Defines Potentially Targetable Therapeutic Pathways
RNA-seq (gene expression) · human · 265 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
- 265 samples: 265 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
- A blood-based transcriptomic signature stratifies severe Crohn's disease and defines potentially targetable therapeutic pathwaysFrontiers in gastroenterology (Lausanne, Switzerland) · 2023
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE217352_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA898420 and SRA study SRP406883. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 265 sample titles: 265 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.
- GSM6715698 Patient226432_CD_Surgery_LPT
- GSM6715699 Patient226432_CD_Surgery_PBT
- GSM6715700 Patient226946_CD_Surgery_LPT
- GSM6715701 Patient226946_CD_Surgery_PBT
- GSM6715702 Patient224667_CD_Surgery_LPT
- GSM6715703 Patient224667_CD_Surgery_PBT
- GSM6715704 Patient226434_CD_Surgery_LPT
- GSM6715705 Patient226434_CD_Surgery_PBT
- GSM6715706 Patient239853_CD_Surgery_LPT
- GSM6715707 Patient239853_CD_Surgery_PBT
- GSM6715708 Patient227440_CD_PostSurgery_PBT
- GSM6715709 Patient226425_CD_Surgery_LPT
- GSM6715710 Patient226425_CD_Surgery_PBT
- GSM6715711 Patient225295_CD_Surgery_LPT
- GSM6715712 Patient225295_CD_Surgery_PBT
- GSM6715713 Patient226536_CD_Surgery_LPT
- GSM6715714 Patient226536_CD_Surgery_PBT
- GSM6715715 Patient227440_CD_Surgery_LPT
- GSM6715716 Patient226260_CD_Surgery_LPT
- GSM6715717 Patient226260_CD_Surgery_PBT
- GSM6715718 Patient226218_CD_Surgery_LPT
- GSM6715719 Patient226218_CD_Surgery_PBT
- GSM6715720 Patient226262_CD_Surgery_LPT
- GSM6715721 Patient226262_CD_Surgery_PBT
- GSM6715722 Patient226536_CD_PostSurgery_PBT
- GSM6715723 Patient225781_CD_Surgery_LPT
- GSM6715724 Patient225781_CD_Surgery_PBT
- GSM6715725 Patient226946_CD_PostSurgery_PBT
- GSM6715726 Patient226432_CD_PostSurgery_PBT
- GSM6715727 Patient226001_CD_Surgery_LPT
- GSM6715728 Patient226001_CD_Surgery_PBT
- GSM6715729 Patient226649_CD_Surgery_LPT
- GSM6715730 Patient226649_CD_Surgery_PBT
- GSM6715731 Patient225302_CD_Surgery_LPT
- GSM6715732 Patient225302_CD_Surgery_PBT
- GSM6715733 Patient225601_CD_Surgery_LPT
- GSM6715734 Patient225601_CD_Surgery_PBT
- GSM6715735 Patient224667_CD_PostSurgery_PBT
- GSM6715736 Patient227596_CD_Surgery_LPT
- GSM6715737 Patient227596_CD_Surgery_PBT
+ 225 more — browse all 265 samples with per-sample file links →
- GSE309430 Blood-Based Gene Signatures Associated with Therapeutic Response to Anti-TNF Therapy in Rheumatoid Arthritis: A Combined Meta-Analytical and Machine Learning Approach 8 samples shares blood-based, therapeutic, signature
- GSE215274 Identification of Whole Blood Gene Expression Signature to Predict the Therapeutic Effect of Nintedanib in Idiopathic Pulmonary Fibrosis 177 samples shares therapeutic, signature
- GSE235738 Alveolar Soft Part Sarcoma is driven by ASPSCR1::TFE3-dependent and therapeutically targetable transcriptional programs [RNA-Seq] 35 samples shares therapeutic, targetable
- GSE263089 ESR1 and p53 Interactome Defines Mechanisms of Therapeutic Response to Tamoxifen Therapy in Luminal Breast Cancer Patients 35 samples shares therapeutic, defines
- GSE269942 YAP1 status defines two intrinsic subtypes of LCNEC with distinct molecular features and therapeutic vulnerabilities 12 samples shares therapeutic, defines
- GSE68086 RNA-seq of tumor-educated platelets enables blood-based pan-cancer, multiclass and molecular pathway cancer diagnostics 285 samples shares blood-based
- GSE309595 Longitudinal Analysis of Multiple Myeloma: Therapeutic Response and Immune Microenvironment Dynamics in the Context of Tumor Heterogeneity [scRNA-seq] 270 samples shares therapeutic
- GSE318816 Blood-based Molecular Endotyping of Fibrotic Hypersensitivity Pneumonitis Identifies Two Immune Subtypes with Divergent Clinical Outcomes 126 samples shares blood-based
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.