Analysis of rectal transcriptome in ulcerative colitis (UC) patients who received tofacitinib
RNA-seq (gene expression) · human · 51 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
- 51 samples: 51 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
- Tofacitinib Uptake by Patient-Derived Intestinal Organoids Predicts Individual Clinical ResponsivenessGastroenterology · 2024
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 GSE245890_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 PRJNA1030353 and SRA study SRP467554. 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 51 sample titles: 51 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.
- GSM7850356 Rectum biopsies, week 24, no replicates P01_W24
- GSM7850357 Rectum biopsies, week 0, no replicates P02_W0
- GSM7850358 Rectum biopsies, week 24, no replicates P03_W24
- GSM7850359 Rectum biopsies, week 24, no replicates P05_W24
- GSM7850360 Rectum biopsies, week 24, no replicates P07_W24
- GSM7850361 Rectum biopsies, week 24, no replicates P08_W24
- GSM7850362 Rectum biopsies, week 24, no replicates P11_W24
- GSM7850363 Rectum biopsies, week 24, no replicates P13_W24
- GSM7850364 Rectum biopsies, week 24, no replicates P14_W24
- GSM7850365 Rectum biopsies, week 0, no replicates P16_W0
- GSM7850366 Rectum biopsies, week 24, no replicates P16_W24
- GSM7850367 Rectum biopsies, week 0, no replicates P18_W0
- GSM7850368 Rectum biopsies, week 24, no replicates P18_W24
- GSM7850369 Rectum biopsies, week 24, no replicates P19_W24
- GSM7850370 Rectum biopsies, week 0, no replicates P20_W0
- GSM7850371 Rectum biopsies, week 24, no replicates P20_W24
- GSM7850372 Rectum biopsies, week 0, no replicates P21_W0
- GSM7850373 Rectum biopsies, week 0, no replicates P22_W0
- GSM7850374 Rectum biopsies, week 24, no replicates P22_W24
- GSM7850375 Rectum biopsies, week 0, no replicates P23_W0
- GSM7850376 Rectum biopsies, week 0, no replicates P24_W0
- GSM7850377 Rectum biopsies, week 24, no replicates P24_W24
- GSM7850378 Rectum biopsies, week 0, no replicates P25_W0
- GSM7850379 Rectum biopsies, week 24, no replicates P25_W24
- GSM7850380 Rectum biopsies, week 0, no replicates P26_W0
- GSM7850381 Rectum biopsies, week 24, no replicates P26_W24
- GSM7850382 Rectum biopsies, week 24, no replicates P27_W24
- GSM7850383 Rectum biopsies, week 24, no replicates P28_W24
- GSM7850384 Rectum biopsies, week 0, no replicates P29_W0
- GSM7850385 Rectum biopsies, week 0, no replicates P30_W0
- GSM7850386 Rectum biopsies, week 0, no replicates P31_W0
- GSM7850387 Rectum biopsies, week 0, no replicates P32_W0
- GSM7850388 Rectum biopsies, week 0, no replicates P33_W0
- GSM7850389 Rectum biopsies, week 0, no replicates P34_W0
- GSM7850390 Rectum biopsies, week 0, no replicates P35_W0
- GSM7850391 Rectum biopsies, week 0, no replicates P37_W0
- GSM7850392 Rectum biopsies, week 0, no replicates P38_W0
- GSM7850393 Rectum biopsies, week 24, no replicates P38_W24
- GSM7850394 Rectum biopsies, week 0, no replicates P39_W0
- GSM7850395 Rectum biopsies, week 24, no replicates P39_W24
+ 11 more — browse all 51 samples with per-sample file links →
- GSE253006 Differential effects of tofacitinib on macrophage activation contribute to lack of response in ulcerative colitis patients 23 samples shares tofacitinib, ulcerative, colitis
- GSE296969 Gene expression at single cell level of stromal cells from the distal colon of normal sites of colorectal cancer and inflamed sites of ulcerative colitis. 13 samples shares ulcerative, colitis, rectal
- GSE235236 Bulk RNAseq expression data of colon biopsies from intestinal mucosa of non-IBD controls and patients with Crohn's disease or ulcerative colitis 56 samples shares ulcerative, colitis
- GSE276170 Transcriptomic profiles of biopsy-derived colon epithelial organoids from pediatric patients with ulcerative colitis 48 samples shares ulcerative, colitis
- GSE224758 Gene expression profiling of colon biopsies from ulcerative colitis patients and healthy volunteers 22 samples shares ulcerative, colitis
- GSE298464 Single-cell RNA sequencing reveals ulcerative colitis patients’ response to anti-TNF-α therapy 16 samples shares ulcerative, colitis
- GSE334803 RNA sequencing of colonic tissues from ulcerative colitis patients and healthy controls 12 samples shares ulcerative, colitis
- GSE296485 The RNA-seq of Ulcerative colitis patients and health 9 samples shares ulcerative, colitis
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.