GEO series

Effect of FcRγ on gene expression profile of naïve and IL-15 treated NK cells

GSE287306 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/09/03 Platform GPL21626

At a glance

RNA-seq (gene expression) · mouse · 24 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: Mus musculus (mouse)
Samples: 24 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.
Paper: FcRγ-Dependent NK Cell Licensing through CD244 Promotes Antitumor ImmunityCancer immunology research · 2025

Summary (written by the submitters)

Here, we aimed to study the NK cell molecular signatures under the control of FcRγ and how these signatures are regulated by IL-15 and the tumour microenvironment (TME). To investigate this, we obtained purified splenic NK cells from naïve wild-type (WT) and FcRγ-deficient (FcRγ–/–, KO) mice cultured in the presence or absence of IL-15 for three days.

Read the full summary ↓

To obtain NK cells from the TME, NK cells were purified from tumour-bearing lungs of WT and KO (FcRγ–/–) mice, which were intravenously injected with B16F10 cells two weeks earlier. Naïve NK cells (without any IL-15 treatment) were used as the control group. Next, we performed bulk RNA sequencing (RNA-seq) on six groups of NK cells for gene expression profiling: naive WT, naive KO (FcRγ–/–), IL-15-treated WT, IL-15-treated KO (FcRγ–/–), tumour WT, and tumour KO (FcRγ–/–).

Published in

FcRγ-Dependent NK Cell Licensing through CD244 Promotes Antitumor Immunity

Duhan V, Gomez MR, Le TT et al. · Cancer immunology research 2025 · PMID 40924773 · doi:10.1158/2326-6066.CIR-25-0174

This dataset

Open GSE287306 in finder → Find more mouse 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 GSE287306_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 PRJNA1212070 and SRA study SRP558129. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40924773) ↗

Study design

6 conditions, mostly with about 4 replicates each

WT NK cells, naïve, ×4 WT NK cells, IL-15 treated, ×4 KO NK cells, naïve, ×4 KO NK cells, IL-15 treated, ×4 WT NK cells, ×4 KO NK cells, ×4

Supports a case/control comparison: 4 samples read as cases, 8 as controls.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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

GSM8743576 WT NK cells, naïve, rep 1 WT NK cells, naïve,
GSM8743577 WT NK cells, naïve, rep 2 WT NK cells, naïve,
GSM8743578 WT NK cells, naïve, rep 3 WT NK cells, naïve,
GSM8743579 WT NK cells, naïve, rep 4 WT NK cells, naïve,
GSM8743580 WT NK cells, IL-15 treated, rep 1 WT NK cells, IL-15 trea…
GSM8743581 WT NK cells, IL-15 treated, rep 2 WT NK cells, IL-15 trea…
GSM8743582 WT NK cells, IL-15 treated, rep 3 WT NK cells, IL-15 trea…
GSM8743583 WT NK cells, IL-15 treated, rep 4 WT NK cells, IL-15 trea…
GSM8743584 KO NK cells, naïve, rep 1 KO NK cells, naïve,
GSM8743585 KO NK cells, naïve, rep 2 KO NK cells, naïve,
GSM8743586 KO NK cells, naïve, rep 3 KO NK cells, naïve,
GSM8743587 KO NK cells, naïve, rep 4 KO NK cells, naïve,
GSM8743588 KO NK cells, IL-15 treated, rep 1 KO NK cells, IL-15 trea…
GSM8743589 KO NK cells, IL-15 treated, rep 2 KO NK cells, IL-15 trea…
GSM8743590 KO NK cells, IL-15 treated, rep 3 KO NK cells, IL-15 trea…
GSM8743591 KO NK cells, IL-15 treated, rep 4 KO NK cells, IL-15 trea…
GSM8743592 WT NK cells, rep 1 WT NK cells,
GSM8743593 WT NK cells, rep 2 WT NK cells,
GSM8743594 WT NK cells, rep 3 WT NK cells,
GSM8743595 WT NK cells, rep 4 WT NK cells,
GSM8743596 KO NK cells, rep 1 KO NK cells,
GSM8743597 KO NK cells, rep 2 KO NK cells,
GSM8743598 KO NK cells, rep 3 KO NK cells,
GSM8743599 KO NK cells, rep 4 KO NK cells,

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