Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - CD45 scRNA-Seq
Single-cell RNA-seq · human · 15 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 15 samples: 14 distinct titles, 1 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
- 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 GSE189754_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.
Also filed as BioProject PRJNA784422 and SRA study SRP348343. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 15 sample titles: 14 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.
- GSM5706743 GI3031 (SA)
- GSM5706744 GI3060 (SB)
- GSM5706745 GI3126 (SC)
- GSM5706746 GI3236 (SD)
- GSM5706747 IBD3736NI
- GSM5706748 IBD3736_I
- GSM5706749 IBD3552_NI
- GSM5706750 IBD3552_I
- GSM5706751 IBD2368_NI
- GSM5706752 IBD2368_I
- GSM5706753 IBD2218_NI
- GSM5706754 IBD2218_I
- GSM5706755 GI3410
- GSM5706756 GI3409
- GSM5706757 GI3369 (GI 3726)
- 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, scrna-seq, spatial, therapy
- 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, scrna-seq, spatial, therapy
- GSE189185 Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis. 117 samples shares microdomains, ulcerative, checkpoint, divergent, spatial, therapy
- GSE189184 Divergent spatial microdomains drive inflammation and repair in Ulcerative and Immune Checkpoint Therapy Colitis - Spatial Transcriptomics 16 samples shares microdomains, ulcerative, checkpoint, divergent, spatial, therapy
- GSE287541 Transcriptomic and proteomic characterization of cell and protein biomarkers of checkpoint inhibitor-induced liver injury [scRNA-seq] 92 samples shares checkpoint, scrna-seq
- GSE318297 Dynamic interaction between tentacle-tethered microdomains in Integrator and NELF regulates the promoter-proximal pause checkpoint [RNA-Seq] 32 samples shares microdomains, checkpoint
- GSE78220 mRNA expressions in pre-treatment melanomas undergoing anti-PD-1 checkpoint inhibition therapy 28 samples shares checkpoint, therapy
- GSE272294 Decoding the immune checkpoint signatures in human atherosclerosis: implications of type 2 diabetes and lipid-lowering intervention [human PBMC scRNA-Seq] 24 samples shares checkpoint, scrna-seq
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.