GEO series

Temporal tracking of microglia activation in neurodegeneration at single-cell resolution

GSE103334 Mus musculus (mouse) Single-cell RNA-seq 2208 samples Submitted 2017/10/10 Platform GPL13112

At a glance

Single-cell RNA-seq · mouse · 2208 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: 2208 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)

In this study, we used single-cell RNA-sequencing to gain unprecedented insight into the phenotypic heterogeneity and the transcriptional dynamics of microglia cells during the progression of neurodegeneration. Briefly, by using a severe neurodegeneration mouse model with Alzheimer’s-like pathology and phenotypes (CK-p25 model), we surveyed microglia activation by RNA sequencing longitudinally at fine temporal- and single-cell resolution.

Read the full summary ↓

In summary, our work identified previously unobserved heterogeneity in the response of microglia to neurodegeneration, discovered novel microglia cell states, revealed the trajectory of cellular reprogramming of microglia in response to neurodegeneration, and uncovered the underlying transcriptional programs. These insights into the molecular programs underlying microglia activation provided by our study may pave the way for designing new rational and efficient strategies to treat Alzheimer’s and other neurodegenerative diseases.

This dataset

Open GSE103334 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 GSE103334_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 PRJNA401847 and SRA study SRP124513. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 29020624) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 2208 more — browse all 2208 samples with per-sample file links →

Datasets on a similar topic

GSE277789 Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq-add] 830 samples shares single-cell, resolution, temporal
GSE276180 Single-cell temporal landscape of tumor microenvironment of lung cancer and lung metastases 37 samples shares single-cell, temporal
GSE150817 Transcriptional dynamics of the murine heart during perinatal development at single-cell resolution 30 samples shares single-cell, resolution
GSE310028 Dissecting Semaglutide-dependent transcriptome response in obesity and osteoarthritis across tissues at single-cell resolution 28 samples shares single-cell, resolution
GSE275408 Reactivation of mTOR signaling slows neurodegeneration in a lysosomal storage disease 24 samples shares neurodegeneration, activation
GSE249931 Temporal single-cell profiling of distinct mesenchymal, epithelial, endothelial, and immune cell lineages in the lung after injury 17 samples shares single-cell, temporal
GSE269183 Microglia contribute to polyG-dependent neurodegeneration in neuronal intranuclear inclusion disease II 16 samples shares neurodegeneration, microglia
GSE319238 Single-cell transcriptomic analysis of microglia and brain cells after ischemic stroke 12 samples shares single-cell, microglia

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.