Single nucleus RNA sequencing of the cerebral cortex from genetically diverse inbred mouse strains reveals differences in pericyte and endothelial cell composition
Single-nucleus RNA-seq · mouse · 16 samples
- What it is
- Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
- Organism
- Mus musculus (mouse)
- Samples
- 16 samples: 16 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.
- Paper
- Single nucleus RNA sequencing of the cerebral cortex from genetically diverse inbred mouse strains reveals differences in pericyte and endothelial cell compositionPloS one · 2025
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 GSE263649_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 PRJNA1098645 and SRA study SRP500755. 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 16 sample titles: 16 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.
- GSM8195994 sublibrary1, batch 1, scRNAseq
- GSM8195995 sublibrary2, batch 1, scRNAseq
- GSM8195996 sublibrary3, batch 1, scRNAseq
- GSM8195997 sublibrary 4, batch 1, scRNAseq
- GSM8195998 sublibrary 5, batch 1, scRNAseq
- GSM8195999 sublibrary 6, batch 1, scRNAseq
- GSM8196000 sublibrary 7, batch 1, scRNAseq
- GSM8196001 sublibrary 8, batch 1, scRNAseq
- GSM8196002 sublibrary 9, batch 2, scRNAseq
- GSM8196003 sublibrary 10, batch 2, scRNAseq
- GSM8196004 sublibrary 11, batch 2, scRNAseq
- GSM8196005 sublibrary 12, batch 2, scRNAseq
- GSM8196006 sublibrary 13, batch 2, scRNAseq
- GSM8196007 sublibrary 14, batch 2, scRNAseq
- GSM8196008 sublibrary 15, batch 2, scRNAseq
- GSM8196009 sublibrary 16, batch 2, scRNAseq
- GSE333520 The flame retardant triphenyl phosphate induces varying responses in genetically diverse mouse induced pluripotent stem cells 436 samples shares genetically, diverse
- GSE272039 Multi-tissue single cell profiling of genetically diverse mouse models reveals mechanisms of resilience to obesity and diabetes [scRNA_seq_adipose] 21 samples shares genetically, diverse
- GSE325187 Senescent Endothelial Cells in Cerebral Microcirculation Are Key Drivers of Age-Related Blood-Brain Barrier Disruption, Microvascular Rarefaction, and Neurovascular Coupling Impairment in Mice 20 samples shares endothelial, cerebral
- GSE271769 Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype 16 samples shares endothelial, cerebral
- GSE192687 Single-cell RNAseq analysis of renal endothelial cells in murine diabetic nephropathy 5464 samples shares endothelial
- GSE294832 Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part10] 1000 samples shares genetically
- GSE294911 Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice [part14] 1000 samples shares genetically
- GSE294535 Modular neuroinflammatory network discovery from large-scale phenotypic screening in genetically heterogeneous mice[part5] 1000 samples shares genetically
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.