Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humans
RNA-seq (gene expression) · human · 28 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
- 28 samples: 24 distinct titles, 2 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
- Stem-like T cells are associated with the pathogenesis of ulcerative colitis in humansNature immunology · 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 GSE235665_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 PRJNA986863 and SRA study SRP445515. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 28 sample titles: 24 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.
- GSM7507204 006_10x_048_JiCh03_A_Gex
- GSM7507205 007_10x_048_JiCh03_C_Gex
- GSM7507206 008_10x_048_JiCh03_N_Gex
- GSM7507207 009_10x_048_JiCh03_B_Gex
- GSM7507208 010_10x_048_JiCh03_A_TCR
- GSM7507209 011_10x_048_JiCh03_C_TCR
- GSM7507210 012_10x_048_JiCh03_N_TCR
- GSM7507211 013_10x_048_JiCh03_B_TCR
- GSM7507212 014_10x_048_JiCh03_A_CITE
- GSM7507213 015_10x_048_JiCh03_C_CITE
- GSM7507214 016_10x_048_JiCh03_N_CITE
- GSM7507215 017_10x_048_JiCh03_B_CITE
- GSM7507216 10x_035_JiCh_CITE
- GSM7507217 10x_035_JiCh_Gex
- GSM7507218 10x_035_JiCh_TCR
- GSM7507219 10x_042_JiCh02_CITE
- GSM7507220 10x_042_JiCh02_Gex
- GSM7507221 10x_042_JiCh02_TCR
- GSM7507222 YiLi04_Mo_12H_CITE
- GSM7507223 YiLi04_Mo_12H_Gex
- GSM8218597 Lamina propria, CD4 T cell, TCF7-, rep1
- GSM8218598 Lamina propria, CD4 T cell, TCF7-, rep2
- GSM8218599 Lamina propria, CD4 T cell, TCF7-, rep3
- GSM8218600 Lamina propria, CD4 T cell, TCF7+, rep1
- GSM8218601 Lamina propria, CD4 T cell, TCF7+, rep2
- GSM8218602 Lamina propria, CD4 T cell, TCF7+, rep3
- GSM8219571 YiLi07_Mo_CD8, Gex
- GSM8219572 YiLi07_Mo_CD8, CITE
- GSE306845 Accute and repeated DSS exposure induce distinct immune responses with differential relevance to human Ulcerative Colitis 10 samples shares ulcerative, colitis
- GSE224478 ETMR stem-like state and chemo-resistance are supported by perivascular cells at single-cell resolution 51 samples shares stem-like
- GSE224475 ETMR stem-like state and chemo-resistance are supported by perivascular cells at single-cell resolution (human+murine organoids subset) 21 samples shares stem-like
- GSE306154 The Colon Contains an Immature/Intermediate iNKT Cell Population That is Expandable by CD1d Expressing Goblet Cells and Can be Protective in Colitis 9 samples shares 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.