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TCR signaling via NFATc1 constrains IL-15-induced NK-like activation of human memory CD8+ T cells [RNAseq_CD3_48H]

GSE305714 Homo sapiens (human) RNA-seq (gene expression) 40 samples Submitted 2025/10/25 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 40 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
40 samples: 10 × CCR7- memory CD8+ T cells, No treatment, 48hours, vs 10 × CCR7- memory CD8+ T cells, IL-15, 48hours, vs 10 × CCR7- memory CD8+ T cells, anti-CD3, 48hours, vs 10 × CCR7- memory CD8+ T cells, IL-15 + anti-CD3, 48hours,Groups 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)
Here we investigated the regulatory mechanisms of TCR-independent bystander activation and NK-like cytotoxicity of human CCR7- memory CD8+ T cells. We found that TCR signals suppressed characteristic features of IL-15-induced CD8+ T-cell activation, including upregulated NKG2D expression and genes related to NK cytotoxicity and IFN response.
Read the full summary ↓
Moreover, ionomycin suppressed IL-15-induced bystander activation and NK-like cytotoxicity, indicating that Ca2+-calcineurin signaling is responsible for TCR-mediated suppression of IL-15-induced bystander activation. NFATc1 suppressed IL-15-induced bystander activation via binding to AP-1 that is necessary for the IL-15-induced upregulation of NK cytotoxicity-related genes. Consistently, calcineurin inhibitors enhanced IL-15-induced NKG2D expression under concurrent TCR stimulation. Additionally, we defined genes upregulated by IL-15 and downregulated by concurrent TCR signals as an IL-15-induced bystander activation gene set, which was upregulated in bystander CD8+ T cells from patients with hepatitis A virus infection. Our findings open avenues for investigating bystander CD8+ T-cell activation and its regulation in pathological conditions.
This dataset
Open GSE305714 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 GSE305714_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 PRJNA1307499 and SRA study SRP609718. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
10 × CCR7- memory CD8+ T cells, No treatment, 48hours, vs 10 × CCR7- memory CD8+ T cells, IL-15, 48hours, vs 10 × CCR7- memory CD8+ T cells, anti-CD3, 48hours, vs 10 × CCR7- memory CD8+ T cells, IL-15 + anti-CD3, 48hours,

Supports a between-group comparison across 40 samples.

How we read this: 4 replicated groups read from 40 sample titles; they account for 40 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
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