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Eomes expression identifies the early bone marrow precursor to classical NK cells

GSE245062 Mus musculus (mouse) RNA-seq (gene expression) 23 samples Submitted 2024/12/31 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 23 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
23 samples: 6 × RNA_ILCP vs 6 × RNA_NKP vs 6 × RNA_NK vs 5 × RNA_EILPGroups 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
Eomes expression identifies the early bone marrow precursor to classical NK cellsNature immunology · 2024
Summary (written by the submitters)
Classical NK cells are the prototypical type 1 innate lymphocytes mounting cytolytic and IFNγ responses to intracellular pathogens and tumors. A similar but distinct population termed ILC1 was recently described, differing from NK cells in multiple though relatively subtle ways, including tissue residency vs recirculation, and levels of NK receptors.
Read the full summary ↓
Whether the differences reflect distinct lineages or mere variations in program expression is not fully understood. Here, using transcription factor reporter mice and cell transfers of bone marrow precursors, we found that, upon transfer in vivo, Eomes-expressing, lineage-negative, NK receptor-negative cells acquired properties typically associated with classical NK cells including the capacity to prevent metatstatic disease. In contrast, as previously reported, PLZF-expressing cells mostly gave rise to ILC1 cells. These findings identify the Eomes-expressing NK precursor as the long-elusive bone marrow precursor to classical NK cells, and demonstrate that the NK and ILC1 lineages diverge early during development.
Published in
Eomes expression identifies the early bone marrow precursor to classical NK cells
Liang Z, Anderson HD, Locher V et al. · Nature immunology 2024 · PMID 38871999 · doi:10.1038/s41590-024-01861-6
This dataset
Open GSE245062 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 GSE245062_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 PRJNA1026879 and SRA study SRP465620. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38871999) ↗
Study design
6 × RNA_ILCP vs 6 × RNA_NKP vs 6 × RNA_NK vs 5 × RNA_EILP

Supports a between-group comparison across 23 samples.

How we read this: 4 replicated groups read from 23 sample titles; they account for 23 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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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.