Impact of severe traumatic brain injury (TBI) on cerebral blood flow and the endothelial cell phenotype
Single-cell RNA-seq · mouse · 16 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. 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
- Severe traumatic brain injury temporally affects cerebral blood flow, endothelial cell phenotype, and ciliabioRxiv : the preprint server for biology · 2024
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 GSE271769_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 PRJNA1133059 and SRA study SRP518641. 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.
- GSM8384860 Post-TBI day 1 biological replicate 1, scRNAseq
- GSM8384861 Post-TBI day 1 biological replicate 2, scRNAseq
- GSM8384862 Post-TBI day 1 biological replicate 3, scRNAseq
- GSM8384863 Post-TBI day 1 biological replicate 4, scRNAseq
- GSM8384864 Post-TBI day 7 biological replicate 1, scRNAseq
- GSM8384865 Post-TBI day 7 biological replicate 2, scRNAseq
- GSM8384866 Post-TBI day 7 biological replicate 3, scRNAseq
- GSM8384867 Post-TBI day 7 biological replicate 4, scRNAseq
- GSM8384868 Post-TBI day 28 biological replicate 1, scRNAseq
- GSM8384869 Post-TBI day 28 biological replicate 2, scRNAseq
- GSM8384870 Post-TBI day 28 biological replicate 3, scRNAseq
- GSM8384871 Post-TBI day 28 biological replicate 4, scRNAseq
- GSM8384872 No-TBI biological replicate 1, scRNAseq
- GSM8384873 No-TBI biological replicate 2, scRNAseq
- GSM8384874 No-TBI biological replicate 3, scRNAseq
- GSM8384875 No-TBI biological replicate 4, scRNAseq
- GSE245683 ATAC-seq of mouse cortex undergoing early degradation after traumatic brain injury (TBI) 12 samples shares tbi, traumatic, injury
- GSE285890 Sex and genotype affect mouse hippocampal gene expression in response to blast-induced traumatic brain injury 96 samples shares traumatic, injury
- GSE318815 Differential sex-dependent responses of circulating steroid hormones and cortical gene expression in a preclinical traumatic brain injury model 88 samples shares traumatic, injury
- GSE302808 Depletion of Peripheral Monocytes Alters Long-Term Gene Expression in Microglia in a Murine Model of Traumatic Brain Injury 84 samples shares traumatic, injury
- GSE310244 Dynamic Resilience: Stress Phenotypes and Their Impact on Opioid-Taking Behavior, Brain Activity, and Gene Expression 68 samples shares phenotype, impact
- 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 traumatic, injury
- GSE276647 Gene expression profile of microglia following traumatic brain injury and nasal anti-CD3 treatment at acute and chronic timepoints 54 samples shares traumatic, injury
- GSE276182 NF-κB activation in astrocytes critically affects wound regeneration after traumatic brain injury 51 samples shares traumatic, injury
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.