Projects  /  07  /  CD4 CTL

CD4 CTL.

Cytotoxic CD4⁺ T cells across public scRNA-seq atlases. R, Seurat, and a long evening reading Phan, Collora and Upadhyay — compute by SklepCentrum.

Research 10x Genomics Seurat
Pipeline
10x · Seurat
Compute
Solek-1 · K8s
Refs
Phan · Collora · Upadhyay
Status
analysis
What CD4 CTL cells are — schematic
CD4 CTL · what we are looking at · 2025
Overview

Cytotoxic CD4 — finding them in the data.

Most CD4⁺ T cells help. A small subset kills directly — the cytotoxic CD4 (CD4 CTL) population. They show up in chronic infection, in tumour infiltrates, in older donors. They are interesting and they are stubborn to define.

We are pulling published 10x Genomics scRNA-seq datasets, re-running them through a uniform Seurat pipeline on SklepCentrum, and comparing how each paper's gating actually overlaps in transcriptional space. Phan, Collora and Upadhyay are the three reference frames we keep coming back to.

This is the project that justified the single-core monster on Solek-1.

Figures

Figures we are working with.

10x Genomics input — droplet schematic.
What CD4 CTL is, in one diagram.
RStudio session — Seurat pipeline.
Collora et al. — CD4 CTL signature.
Phan et al. — gating.
Upadhyay et al. — CD4 CTL panel.
Upadhyay et al. — overall.
Cross-paper comparison — overlap of gated populations.
Specifications

The pipeline.

Input10x Genomics scRNA-seq · public datasets
ToolingR · Seurat · RStudio
ComputeSolek-1 · scheduled as a K8s job on SklepCentrum
ReferencesPhan · Collora · Upadhyay
Goaluniform re-analysis · cross-paper signature overlap
Statusanalysis
Back to · all projects All projects