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Gene expression profile of NK cells sorted from the lymph node of tumor free C57BL/6J mice and tumor bearing lymph node in Diffuse large B cell lymphoma model of lymphatic or hematogenous.

GSE308924 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/03/23 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 4 × NK cells from tumor free lymph node vs 4 × NK cells from the Lymphatic model of dissemination vs 4 × NK cells from the Hematogenous model of disseminationGroups 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)
The cellular components of the tumor microenvironment (TME) in non-Hodgkin B cell lymphoma demonstrate remarkable diversity. Recent evidence suggests that the spatial organization of malignant, immune and stromal cells within the TME is associated with clinical outcome and response to therapy. Yet, whether tumor cells distribution within the distinct nodal compartments, following lymphatic or hematogenous dissemination further influence the shaping of the TME and the antitumoral immune response remains unclear.
Read the full summary ↓
We used Bulk RNA sequencing to analyze the diversity transcriptomic profiles of NK cells in 3 different conditions.
This dataset
Open GSE308924 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 GSE308924_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 PRJNA1333417 and SRA study SRP625605. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
4 × NK cells from tumor free lymph node vs 4 × NK cells from the Lymphatic model of dissemination vs 4 × NK cells from the Hematogenous model of dissemination

Supports a between-group comparison across 12 samples.

How we read this: 3 replicated groups read from 12 sample titles; they account for 12 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.