Single cell RNA-seq of mouse brain vascular cells with Smart-seq2 method
Single-cell RNA-seq · mouse · 391 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
- 391 samples: 391 × 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 GSE311449_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 PRJNA1369483 and SRA study SRP648822. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 391 samples.
How we read this: 1 replicated groups read from 391 sample titles; they account for 391 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.
- GSM9325093 Brain single cell 1 Brain single cell
- GSM9325094 Brain single cell 2 Brain single cell
- GSM9325095 Brain single cell 3 Brain single cell
- GSM9325096 Brain single cell 4 Brain single cell
- GSM9325097 Brain single cell 5 Brain single cell
- GSM9325098 Brain single cell 6 Brain single cell
- GSM9325099 Brain single cell 7 Brain single cell
- GSM9325100 Brain single cell 8 Brain single cell
- GSM9325101 Brain single cell 9 Brain single cell
- GSM9325102 Brain single cell 10 Brain single cell
- GSM9325103 Brain single cell 11 Brain single cell
- GSM9325104 Brain single cell 12 Brain single cell
- GSM9325105 Brain single cell 13 Brain single cell
- GSM9325106 Brain single cell 14 Brain single cell
- GSM9325107 Brain single cell 15 Brain single cell
- GSM9325108 Brain single cell 16 Brain single cell
- GSM9325109 Brain single cell 17 Brain single cell
- GSM9325110 Brain single cell 18 Brain single cell
- GSM9325111 Brain single cell 19 Brain single cell
- GSM9325112 Brain single cell 20 Brain single cell
- GSM9325113 Brain single cell 21 Brain single cell
- GSM9325114 Brain single cell 22 Brain single cell
- GSM9325115 Brain single cell 23 Brain single cell
- GSM9325116 Brain single cell 24 Brain single cell
- GSM9325117 Brain single cell 25 Brain single cell
- GSM9325118 Brain single cell 26 Brain single cell
- GSM9325119 Brain single cell 27 Brain single cell
- GSM9325120 Brain single cell 28 Brain single cell
- GSM9325121 Brain single cell 29 Brain single cell
- GSM9325122 Brain single cell 30 Brain single cell
- GSM9325123 Brain single cell 31 Brain single cell
- GSM9325124 Brain single cell 32 Brain single cell
- GSM9325125 Brain single cell 33 Brain single cell
- GSM9325126 Brain single cell 34 Brain single cell
- GSM9325127 Brain single cell 35 Brain single cell
- GSM9325128 Brain single cell 36 Brain single cell
- GSM9325129 Brain single cell 37 Brain single cell
- GSM9325130 Brain single cell 38 Brain single cell
- GSM9325131 Brain single cell 39 Brain single cell
- GSM9325132 Brain single cell 40 Brain single cell
+ 351 more — browse all 391 samples with per-sample file links →
- 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
- GSE241165 Characterizing the gene expression profiles of 4T1 and 4T1.2 cells at different stages of bone metastsis using SMART-Seq2 technology 1248 samples shares smart-seq2
- GSE303081 A spatial and projection-based transcriptomic atlas of paraventricular hypothalamic cell types (Smart-Seq2) 81 samples shares smart-seq2
- GSE326100 scRNA-seq of mouse cochlea organoid cells 768 samples shares rna-seq
- GSE313761 Single-cell screens identify ADAM12 as a fibroblast checkpoint impeding anti-tumor immunity - scRNA-seq of Adam12CKO Mouse Model CD45- cells 11 samples shares rna-seq
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.