Single cell RNA-seq of mouse brain vascular transcriptomes
Single-cell RNA-seq · mouse · 3186 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
- 3186 samples: 400 × Brain single cellGroups 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 GSE98816_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 PRJNA386336 and SRA study SRP106908. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 400 samples.
How we read this: 1 replicated groups read from the first 400 of 3186 sample titles; they account for 400 of them. 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.
- GSM2612539 Brain single cell 1 Brain single cell
- GSM2612540 Brain single cell 2 Brain single cell
- GSM2612541 Brain single cell 3 Brain single cell
- GSM2612542 Brain single cell 4 Brain single cell
- GSM2612543 Brain single cell 5 Brain single cell
- GSM2612544 Brain single cell 6 Brain single cell
- GSM2612545 Brain single cell 7 Brain single cell
- GSM2612546 Brain single cell 8 Brain single cell
- GSM2612547 Brain single cell 9 Brain single cell
- GSM2612548 Brain single cell 10 Brain single cell
- GSM2612549 Brain single cell 11 Brain single cell
- GSM2612550 Brain single cell 12 Brain single cell
- GSM2612551 Brain single cell 13 Brain single cell
- GSM2612552 Brain single cell 14 Brain single cell
- GSM2612553 Brain single cell 15 Brain single cell
- GSM2612554 Brain single cell 16 Brain single cell
- GSM2612555 Brain single cell 17 Brain single cell
- GSM2612556 Brain single cell 18 Brain single cell
- GSM2612557 Brain single cell 19 Brain single cell
- GSM2612558 Brain single cell 20 Brain single cell
- GSM2612559 Brain single cell 21 Brain single cell
- GSM2612560 Brain single cell 22 Brain single cell
- GSM2612561 Brain single cell 23 Brain single cell
- GSM2612562 Brain single cell 24 Brain single cell
- GSM2612563 Brain single cell 25 Brain single cell
- GSM2612564 Brain single cell 26 Brain single cell
- GSM2612565 Brain single cell 27 Brain single cell
- GSM2612566 Brain single cell 28 Brain single cell
- GSM2612567 Brain single cell 29 Brain single cell
- GSM2612568 Brain single cell 30 Brain single cell
- GSM2612569 Brain single cell 31 Brain single cell
- GSM2612570 Brain single cell 32 Brain single cell
- GSM2612571 Brain single cell 33 Brain single cell
- GSM2612572 Brain single cell 34 Brain single cell
- GSM2612573 Brain single cell 35 Brain single cell
- GSM2612574 Brain single cell 36 Brain single cell
- GSM2612575 Brain single cell 37 Brain single cell
- GSM2612576 Brain single cell 38 Brain single cell
- GSM2612577 Brain single cell 39 Brain single cell
- GSM2612578 Brain single cell 40 Brain single cell
+ 3146 more — browse all 3186 samples with per-sample file links →
- GSE311449 Single cell RNA-seq of mouse brain vascular cells with Smart-seq2 method 391 samples shares vascular, rna-seq, brain
- GSE319252 Eicosapentaenoic Acid Reprograms Cerebrovascular Metabolism and Impairs Repair after Brain Injury, with Relevance to Chronic Traumatic Encephalopathy [mouse_brain_OnurE_RNA-seq] 12 samples shares vascular, rna-seq, brain
- GSE326452 Bulk RNA-seq of mouse brain following closed head injury: role of IL-1R1 signaling 200 samples shares rna-seq, brain
- GSE277487 Single-nucleus RNA-seq of mouse cortex following CCI-induced traumatic brain injury across multiple time points 12 samples shares rna-seq, brain
- GSE300113 Heterogenous microglial reactivity contrasts with stable vascular transcriptional programs in mouse models of Alzheimer’s, CADASIL, and Traumatic Brain Injury (Main dataset) 59 samples shares vascular, brain
- GSE326100 scRNA-seq of mouse cochlea organoid cells 768 samples shares rna-seq
- GSE239602 Single-cell and spatial transcriptomics uncovers the role of senescent vascular cells in pathological arterial remodeling during murine atherosclerosis 82 samples shares vascular
- GSE281126 single nucleus RNA sequencing of cells from across the whole mouse brain in a mouse model of ALS 10 samples shares brain
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.