Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - Spatial Transcriptomics
Spatial transcriptomics · human · 16 samples
- What it is
- Spatial transcriptomicsGene activity measured with its position in a tissue section.
- Organism
- Homo sapiens (human)
- Samples
- 16 samples: 6 × GI vs 3 × PRISE vs 2 × GI 6967_BGroups 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
- Tracking in situ checkpoint inhibitor-bound target T cells in patients with checkpoint-induced colitisCancer cell · 2024
Read the full summary ↓
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 GSE189184_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: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.
Also filed as BioProject PRJNA781903 and SRA study SRP346915. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 3 replicated groups read from 16 sample titles; they account for 11 of them. 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.
- GSM5695828 GI Biobank Corona Recovery 17 (GI 6266)
- GSM5695829 GI Biobank Corona Recovery 15 (GI 6264)
- GSM5695830 PRISE 31 PRISE
- GSM5695831 PRISE 14 PRISE
- GSM5695832 GI 6275 GI
- GSM5695833 PRISE 23 PRISE
- GSM5695834 GI 6967_B8 GI 6967_B
- GSM5695835 GI 6967_B9 GI 6967_B
- GSM5695836 GI 6278 GI
- GSM5695837 GI 6925 GI
- GSM5695838 GI 6658 GI
- GSM5695839 GI 4980 GI
- GSM5695840 BB4652
- GSM5695841 GI 6274 GI
- GSM5695842 GI 3667 (#1)
- GSM5695843 TIP 517
- GSE189185 Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis. 117 samples shares microdomains, ulcerative, checkpoint, divergent, spatial, therapy, colitis, repair
- GSE189040 Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - CD3 scRNA-Seq 24 samples shares microdomains, ulcerative, checkpoint, divergent, spatial, therapy, colitis, repair
- GSE190564 Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - whole tissue scRNA-Seq 62 samples shares microdomains, ulcerative, checkpoint, divergent, spatial, therapy, colitis, repair
- GSE189754 Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - CD45 scRNA-Seq 15 samples shares microdomains, ulcerative, checkpoint, divergent, spatial, therapy, colitis, repair
- GSE298464 Single-cell RNA sequencing reveals ulcerative colitis patients’ response to anti-TNF-α therapy 16 samples shares ulcerative, therapy, colitis
- GSE228597 Immunologic drivers of immune checkpoint inhibitor therapy myocarditis, fatality and anti-tumor response in cancer patients 75 samples shares checkpoint, therapy
- GSE318641 Dynamic interaction between tentacle-tethered microdomains in Integrator and NELF regulates the promoter-proximal pause checkpoint 61 samples shares microdomains, checkpoint
- GSE278119 Clonally expanded effector CD4+ cytotoxic T lymphocytes are associated with severe neurological adverse events after immune checkpoint inhibitor therapy 44 samples shares checkpoint, therapy
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.