GEO series

Selective oxidative protection leads to tissue topological changes orchestrated by macrophage during ulcerative colitis

GSE231993 Homo sapiens (human) Single-cell RNA-seq 12 samples Submitted 2023/05/11 Platform GPL18573

At a glance

Single-cell RNA-seq · human · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 12 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.

Summary (written by the submitters)

Ulcerative colitis (UC) is a chronic inflammatory bowel disorder with cellular heterogeneity. To understand the composition and spatial changes of the UC ecosystem, we use imaging mass cytometry (IMC) and single-cell RNA sequencing (scRNA-seq) to depict the single-cell landscape of the human colon ecosystem. We find tissue topological changes featured with macrophage disappearance reaction (MDR) in the UC region, occurring only for tissue-resident macrophages.

Read the full summary ↓

Reactive oxygen species (ROS) levels are higher in the UC region, but ROS scavenging enzyme SOD2 is barely detected in resident macrophages, resulting in distinct ROS vulnerability for inflammatory macrophages and resident macrophages. Inflammatory macrophages replace resident macrophages and cause a spatial shift of TNF-α production during UC via a cytokine production network formed with T and B cells. Our study discovers the mechanism of MDR of resident macrophages, providing novel mechanistic hints for MDR in other inflammation or infection situations.

This dataset

Open GSE231993 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE231993_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA970371 and SRA study SRP436542. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37344477) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 12 more — browse all 12 samples with per-sample file links →

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