Core Ileal Transcriptome in Pediatric Crohn Disease
RNA-seq (gene expression) · human · 322 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
- 322 samples
- 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.
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 GSE57945_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 PRJNA248469 and SRA study SRP042228. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 322 more — browse all 322 samples with per-sample file links →
- GSE264073 Ileal Enterocyte Brush Border Abnormalities Associate with Progressive Disease Course in Pediatric Crohn’s Disease 152 samples shares pediatric, ileal, crohn
- GSE228360 Spatial and single cell transcriptomics reveals cellular crosstalk changes in ileal Crohn’s disease during inflammation 24 samples shares ileal, crohn
- GSE317503 Reference-guided genome assembly of long non-coding RNA transcripts reveals target genes associated with Crohn’s disease 140 samples shares crohn
- GSE290695 Identification of Crohn’s disease subtypes in single cell RNA sequencing signatures of treatment naïve samples across the gastrointestinal tract 95 samples shares crohn
- GSE266616 Reveal the key mediators of inflammation in Crohn's disease undergoing biological treatments 85 samples shares crohn
- GSE303271 RNA-seq of liver biopsies from patients with pediatric autoimmune liver disease 64 samples shares pediatric
- GSE261086 Multi-Omics Characterization of Colon Mucosa and Submucosa/Wall from Crohn's Disease Patients 52 samples shares crohn
- GSE226039 scRNAseq from pbmc, ileum, and rectal tissue of healthy and crohns disease individuals 46 samples shares crohn
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.