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)
Single-cell RNA-seq · mouse · 34 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
- 34 samples: 34 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.
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE276797_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1159107. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 34 sample titles: 34 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.
- GSM8505924 dCLNs,WT,scRNAseq
- GSM8505925 dCLNs,5xFAD,scRNAseq
- GSM8505926 sCLNs,WT,scRNAseq
- GSM8505927 sCLNs,5xFAD,scRNAseq
- GSM8505928 iLNs,WT,scRNAseq
- GSM8505929 iLNs,5xFAD,scRNAseq
- GSM8505930 dCLNs,CD4,1,scRNAseq
- GSM8505931 dCLNs,CD4,2,scRNAseq
- GSM8505932 dCLNs,sCLNs,iLNs,WT,5xFAD,scRNAseq
- GSM8505933 dCLNs,WT,scRNAseq [GEX]
- GSM8505934 dCLNs,5xFAD,scRNAseq [GEX]
- GSM8505935 sCLNs,WT,scRNAseq [GEX]
- GSM8505936 sCLNs,5xFAD,scRNAseq [GEX]
- GSM8505937 iLNs,WT,scRNAseq [GEX]
- GSM8505938 iLNs,5xFAD,scRNAseq [GEX]
- GSM8505939 dCLNs,sCLNs,iLNs,WT,5xFAD,scRNAseq [GEX]
- GSM8505940 dCLNs,CD4,1,scRNAseq [GEX]
- GSM8505941 dCLNs,CD4,2,scRNAseq [GEX]
- GSM8505942 dCLNs,WT,scRNAseq [vdj_b]
- GSM8505943 dCLNs,5xFAD,scRNAseq [vdj_b]
- GSM8505944 sCLNs,WT,scRNAseq [vdj_b]
- GSM8505945 sCLNs,5xFAD,scRNAseq [vdj_b]
- GSM8505946 iLNs,WT,scRNAseq [vdj_b]
- GSM8505947 iLNs,5xFAD,scRNAseq [vdj_b]
- GSM8505948 dCLNs,sCLNs,iLNs,WT,5xFAD,scRNAseq [vdj_b]
- GSM8505949 dCLNs,WT,scRNAseq [vdj_t]
- GSM8505950 dCLNs,5xFAD,scRNAseq [vdj_t]
- GSM8505951 sCLNs,WT,scRNAseq [vdj_t]
- GSM8505952 sCLNs,5xFAD,scRNAseq [vdj_t]
- GSM8505953 iLNs,WT,scRNAseq [vdj_t]
- GSM8505954 iLNs,5xFAD,scRNAseq [vdj_t]
- GSM8505955 dCLNs,CD4,1,scRNAseq [vdj_t]
- GSM8505956 dCLNs,CD4,2,scRNAseq [vdj_t]
- GSM8505957 dCLNs,sCLNs,iLNs,WT,5xFAD,scRNAseq [vdj_t]
- 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, animals
- GSE276794 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 9 samples shares 5xfad, superficial, transgenic, wild-type, alzheimer, cervical, inguinal, animals
- 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
- GSE75484 Effect of PD-1 immune checkpoint in Alzheimer's disease transgenic mice 25 samples shares transgenic, alzheimer
- GSE276471 Transcriptome regulation in the brain of a transgenic Alzheimer mouse model treated by lactate 24 samples shares transgenic, alzheimer
- GSE290101 Signaling cascades shape functional subpopulations of cortical astrocytes in male wild-type mice and APP/PS1dE9 Alzheimer’s disease model 18 samples shares wild-type, alzheimer
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.