Spatial Transcriptomics of Meningeal Inflammation Reveals Variable Penetrance of Inflammatory Gene Signatures into Adjacent Brain Parenchyma
Spatial transcriptomics · mouse · 11 samples
- What it is
- Spatial transcriptomicsGene activity measured with its position in a tissue section.
- Organism
- Mus musculus (mouse)
- Samples
- 11 samples: 6 × Brain slice, eae, vs 5 × Brain slice, naïve,Groups 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
- Spatial transcriptomics of meningeal inflammation reveals inflammatory gene signatures in adjacent brain parenchymaeLife · 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 GSE236963_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: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.
Also filed as BioProject PRJNA993195 and SRA study SRP448377. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 11 samples.
How we read this: 2 replicated groups read from 11 sample titles; they account for 11 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.
- GSM7589541 Brain slice, naïve, 1 Brain slice, naïve,
- GSM7589543 Brain slice, naïve, 2 Brain slice, naïve,
- GSM7589544 Brain slice, naïve, 3 Brain slice, naïve,
- GSM7589545 Brain slice, naïve, 4 Brain slice, naïve,
- GSM7589546 Brain slice, naïve, 5 Brain slice, naïve,
- GSM7589548 Brain slice, eae, 1 Brain slice, eae,
- GSM7589549 Brain slice, eae, 2 Brain slice, eae,
- GSM7589550 Brain slice, eae, 3 Brain slice, eae,
- GSM7589551 Brain slice, eae, 4 Brain slice, eae,
- GSM7589553 Brain slice, eae, 5 Brain slice, eae,
- GSM7589554 Brain slice, eae, 6 Brain slice, eae,
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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.