Gene expression profile at single cell level of immune cells from the dura mater of naïve C57BL6/N mice and during different phases of EAE.
Single-cell RNA-seq · mouse · 10 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
- 10 samples: 8 distinct titles, 2 of them repeatedGroups 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
- Extrasinusoidal macrophages are a distinct subset of immunologically active dural macrophagesScience immunology · 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 GSE278812_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 PRJNA1168964 and SRA study SRP536642. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 10 sample titles: 8 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.
- GSM8555483 Sinusoidal dura, naïve, replicate 1
- GSM8555484 Sinusoidal dura, EAE onset, replicate 1
- GSM8555485 Sinusoidal dura, EAE peak, replicate 1
- GSM8555486 Extrasinusoidal dura, naïve, replicate 1
- GSM8555487 Extrasinusoidal dura, EAE onset, replicate 1
- GSM8555488 Extrasinusoidal dura, EAE peak, replicate 1
- GSM8555489 Sinusoidal dura, naïve, replicate 2
- GSM8555490 Sinusoidal dura, EAE chronic, replicate 1
- GSM8555491 Extrasinusoidal dura, naïve, replicate 2
- GSM8555492 Extrasinusoidal dura, EAE chronic, replicate 1
- GSE287323 Transcriptomic profiling of oligodendrocytes, astrocytes, and microglia in an experimental autoimmune encephalomyelitis (EAE) model of demyelination 19 samples shares eae
- GSE226609 Mouse lung tissue RNA-Seq from C57Bl6 wild type and ALOX15 KO mice with and without house dust mite (HDM) exposure. 20 samples shares c57bl6
- GSE281907 Spinal cord bulk RNA sequencing of an EAE mouse model of multiple sclerosis 16 samples shares eae
- GSE281176 Spinal cord single-nuclei RNA sequencing of an EAE mouse model of multiple sclerosis 16 samples shares eae
- GSE342137 Comparison of NK cell transcriptomes between C57BL6 and NOD mouse strains 8 samples shares c57bl6
- GSE295428 Spaceflight induces systemic effects on extracellular matrix and immune system in different age-stages 229 samples shares different
- GSE302070 Heterogeneity and Homogeneity in Treg responses to Interleukin-2 [RNAseq2: Differential activation of Immune cell types by IL2-Immunocytokines] 45 samples shares different
- GSE293709 Transcriptome analysis in the prefrontal cortex of different ASD mouse models treated with drug 1565 samples shares different
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.