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Feeder-free generation of CD4 single-positive helper T cells from human iPSCs via stage-specific modulation of Notch and TCR Signaling

GSE316025 Homo sapiens (human) RNA-seq (gene expression) 21 samples Submitted 2026/06/23 Platform GPL28038
At a glance

RNA-seq (gene expression) · human · 21 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
21 samples: 6 conditions, mostly with about 4 replicates eachGroups 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.
Summary (written by the submitters)
Induced pluripotent stem cell (iPSC)-derived T cells (iPS-T cells) represent a promising platform for adoptive immunotherapy, offering an unlimited source of T cells amenable to gene editing and rigorous quality control. While feeder-free in vitro redifferentiation systems have been successfully developed for CD8+ cytotoxic T cells, the generation of CD4+ helper T cells under similar conditions has remained elusive—despite their essential role in sustaining long-term immune responses.
Read the full summary ↓
In this study, we established a feeder-free culture system for the generation of CD4 single-positive (SP) helper T cells from iPSCs, under conditions that exclude TCR signaling, which otherwise biases differentiation toward the cytotoxic lineage. By precisely modulating Notch and integrin signaling in a stage-specific manner, we induced the differentiation of CD4 SP iPS-T cells expressing key helper-associated molecules, including CD40L and ThPOK, capable of promoting dendritic cell maturation. Notably, these cells also acquired cytotoxic activity upon repeated expansion while retaining robust proliferative capacity. Our findings provide a foundation for the scalable and consistent production of both CD4 SP helper and killer T cells from pluripotent stem cells, advancing the potential of iPSC-based immunotherapies.
This dataset
Open GSE316025 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 GSE316025_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: 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 PRJNA1399716. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly with about 4 replicates each
scRNA-seq library of Feeder-free iPS-T cells … ×4 ADT library of Feeder-free iPS-T cells Day ×4 scTCR-seq library of Feeder-free iPS-T cells … ×4 scRNA-seq library of ATO iPS-T cells Day ×3 ADT library of ATO iPS-T cells Day ×3 scTCR-seq library of ATO iPS-T cells Day ×3

Supports a between-group comparison across 21 samples.

How we read this: 6 replicated groups read from 21 sample titles; they account for 21 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.

Samples in this study
Datasets on a similar topic

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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.