Brain endothelial cells with inflammatory signature in CCM disease in hypoxia and normoxia conditions
RNA-seq (gene expression) · mouse · 18 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 18 samples: 5 × Normoxia_KO vs 5 × Hypoxia_KO vs 4 × Normoxia_Flox vs 4 × Hypoxia_FloxGroups 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
- Mild Hypoxia Accelerates Cerebral Cavernous Malformation Disease Through CX3CR1-CX3CL1 SignalingArteriosclerosis, thrombosis, and vascular biology · 2024
Read the full summary ↓
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 GSE261224_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1085778 and SRA study SRP494213. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 4 replicated groups read from 18 sample titles; they account for 18 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.
- GSM8138083 Normoxia_Flox_1 Normoxia_Flox
- GSM8138084 Normoxia_Flox_2 Normoxia_Flox
- GSM8138085 Normoxia_Flox_3 Normoxia_Flox
- GSM8138086 Normoxia_Flox_4 Normoxia_Flox
- GSM8138087 Normoxia_KO_1 Normoxia_KO
- GSM8138088 Normoxia_KO_2 Normoxia_KO
- GSM8138089 Normoxia_KO_4 Normoxia_KO
- GSM8138090 Normoxia_KO_5 Normoxia_KO
- GSM8138091 Normoxia_KO_6 Normoxia_KO
- GSM8138092 Hypoxia_Flox_2 Hypoxia_Flox
- GSM8138093 Hypoxia_Flox_3 Hypoxia_Flox
- GSM8138094 Hypoxia_Flox_4 Hypoxia_Flox
- GSM8138095 Hypoxia_Flox_5 Hypoxia_Flox
- GSM8138096 Hypoxia_KO_1 Hypoxia_KO
- GSM8138097 Hypoxia_KO_2 Hypoxia_KO
- GSM8138098 Hypoxia_KO_3 Hypoxia_KO
- GSM8138099 Hypoxia_KO_4 Hypoxia_KO
- GSM8138100 Hypoxia_KO_5 Hypoxia_KO
- GSE236963 Spatial Transcriptomics of Meningeal Inflammation Reveals Variable Penetrance of Inflammatory Gene Signatures into Adjacent Brain Parenchyma 11 samples shares signature, brain
- GSE300534 Brain Mecp2 Genetic Dosage and Gene Therapy Shape Multi-omics Signatures and Biomarkers in Rett Syndrome [1] 137 samples shares signature, brain
- GSE300536 Brain Mecp2 Genetic Dosage and Gene Therapy Shape Multi-omics Signatures and Biomarkers in Rett Syndrome [2] 137 samples shares signature, brain
- GSE290810 ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits [FACS_SpinalCord_Microglia & LPS_Brain_SpinalCord] 35 samples shares signature, brain
- GSE316502 Transcriptomic Profiling of the Sex-linked Biological Pathways of Severe Pulmonary Arterial Hypertension associated with Endothelial Cell Caveolin-1 Depletion and Chronic Hypoxia 35 samples shares endothelial, hypoxia
- GSE254227 ALS/FTD-linked TBK1 deficiency in microglia induces an aged-like microglial signature and drives social recognition deficits. [FACS_Brain_Microglia] 35 samples shares signature, brain
- 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, brain
- GSE301448 Epigenetic Reactivation of CNS Endothelial Developmental Programs Triggers Adult Brain Angiogenesis, Promotes Post-Stroke Revascularization and Neuroregeneration [RNAseq-Stroke] 18 samples shares endothelial, 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.