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Brain Molecular Mechanisms in Rasmussen Encephalitis

GSE310367 Homo sapiens (human) RNA-seq (gene expression) 49 samples Submitted 2025/11/19 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 49 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
Homo sapiens (human)
Samples
49 samples
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
Brain molecular mechanisms in Rasmussen encephalitisEpilepsia · 2023
Summary (written by the submitters)
Objective: Identify molecular mechanisms in brain tissue of Rasmussen encephalitis (RE) when compared to people with non-RE epilepsy (PWE) and control cases using whole exome sequencing (WES), RNAseq, and proteomics. Methods: Frozen brain tissue (ages 2-19 years) was obtained from control autopsy (n=14), surgical PWE (n=10), and surgical RE cases (n=27).
Read the full summary ↓
We evaluated WES variants in RE associated with epilepsy, seizures, RE, and human leukocyte antigens (HLAs). Differential expression was evaluated by RNAseq (adjusted p<0.05) and label-free quantitative mass spectrometry (false discovery rate<5%) in the three groups. Results: WES revealed no common pathogenic variants in RE, although several rare and likely deleterious variants of unknown significance (VUS; ANGPTL7/MTOR, SCN1A, FCGR3B, MTOR) and more common HLA VUS in >25% RE cases (HLA-DRB1, HLA-DQA2) all with allele frequency <5% in the general population. RNAseq in RE vs. PWE (1516 altered transcripts) revealed significant activation of crosstalk between dendritic and natural killer cells (p=7.94x10-6, z=2.65), in RE vs. control (7466 transcripts) neuroinflammation signaling activation (p=6.31x10-13, z=5.07), and in PWE vs. control (945 transcripts) phagosome formation activation (p=2.00x10-13, z=5.61). Proteomics detected fewer altered targets. Significance: In RE, we identified activated immune signaling pathways and immune cell type annotation enrichment that suggest roles of the innate and adaptive immune responses, as well as HLA variants that may increase vulnerability to RE. Follow up studies could evaluate cell type density and subregional localization associated with top targets, clinical history (neuropathology, disease duration), and whether modulating crosstalk between dendritic and natural killer cells may limit disease progression.
Published in
Brain molecular mechanisms in Rasmussen encephalitis
Leitner DF, Lin Z, Sawaged Z et al. · Epilepsia 2023 · PMID 36336987 · doi:10.1111/epi.17457
This dataset
Open GSE310367 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE310367_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1365836 and SRA study SRP646579. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 36336987) ↗
Study design
A cohort of 49 individual samples

The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Sample titles run RE001 … RE081 and carry no group information.

Samples in this study

+ 9 more — browse all 49 samples with per-sample file links →

Datasets on a similar topic

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