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Gene expression profie at single cell level of immune cells from the deep cervical lymph nodes (dCLNs), superficial cervical lymph nodes (sCLNs), and inguinal lymph nodes (iLNs) of wild-type (WT) and Alzheimer's disease (AD) transgenic animals (5xFAD)

GSE276793 Mus musculus (mouse) Single-cell RNA-seq 9 samples Submitted 2026/07/31 Platform GPL34328Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 9 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
9 samples: 9 samples, each with a distinct title — no replicated groupsGroups 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 dCLNs are lymph nodes specialized in draining cerebrospinal fluid (CSF). We used single cell RNA sequencing (scRNA-seq) to characterize the immune cell populations in the dCLNs compared to other draining lymph nodes. We compared the immune landscape of the dCLNs between healthy WT mice and 5xFAD mice to investigate the role of dCLNs immunity in AD progression. Additionaly, we sequenced the TCR and BCR transcripts to analyze the clonal distribution of T-cells and B-cells in each lymph node.
This dataset
Open GSE276793 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 GSE276793_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1159104 and SRA study SRP531778. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
9 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 9 sample titles: 9 distinct titles with little repetition. 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

Search all mouse RNA-seq datasets in GEO →

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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.