GEO series

Gene expression profile 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)GEX

GSE276794 Mus musculus (mouse) Single-cell RNA-seq 9 samples Submitted 2026/07/31 Platform GPL24247Platform GPL34328

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
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 GSE276794 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 GSE276794_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 PRJNA1159103 and SRA study SRP531777. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 9 more — browse all 9 samples with per-sample file links →

Datasets on a similar topic

GSE276797 Gene expression profile 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) 34 samples shares 5xfad, superficial, transgenic, wild-type, alzheimer, cervical, inguinal
GSE276793 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) 9 samples shares 5xfad, superficial, transgenic, wild-type, alzheimer, cervical, inguinal
GSE276796 Gene expression profile 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 and Alzheimer's disease (AD) transgenic animals (5xFAD)vdj_t 9 samples shares 5xfad, superficial, transgenic, wild-type, alzheimer, cervical, inguinal
GSE276795 Gene expression profile 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 and Alzheimer's disease transgenic animals (5xFAD)vdjb 7 samples shares 5xfad, superficial, transgenic, wild-type, alzheimer, cervical, inguinal
GSE302153 Study of Molecular and Transcriptomic Age-related Changes in the Dorsal and Ventral Areas of Hippocampus in the 5xFAD Mouse Model of Alzheimer’s Disease 32 samples shares 5xfad, alzheimer
GSE296886 Effect of a natural product derivative on gene expression signatures in 5xFAD transgenic mice 25 samples shares 5xfad, transgenic
GSE215439 Effect of metronidazole on microglial gene expression and gut microbiome composition in the 5XFAD mice model of Alzheimer's disease 20 samples shares 5xfad, alzheimer
GSE274214 Splicing transcriptome analysis reveals retained introns in retinal genes of the 5xFAD mouse, suggesting early diagnosis of Alzheimer’s disease through vision impairment 12 samples shares 5xfad, alzheimer

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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.