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Single-nucleus transcriptomics and chromatin accessibility of cell type-specific contributions to the epileptogenic cortex of focal cortical dysplasia type IIIa

GSE266308 Homo sapiens (human) Single-nucleus RNA-seq 14 samples Submitted 2024/10/30 Platform GPL24676
At a glance

Single-nucleus RNA-seq · human · 14 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism
Homo sapiens (human)
Samples
14 samples: 4 × ATAC temporal neocortex, epileptogenic, vs 4 × RNA temporal neocortex, epileptogenic, vs 3 × ATAC temporal neocortex, nonepileptic, vs 3 × RNA temporal neocortex, nonepileptic,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
Excitatory neurons and oligodendrocyte precursor cells are vulnerable to focal cortical dysplasia type IIIa as suggested by single-nucleus multiomicsClinical and translational medicine · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Excitatory neurons and oligodendrocyte precursor cells are vulnerable to focal cortical dysplasia type IIIa as suggested by single-nucleus multiomics
Liu Y, Li Y, Zhang Y et al. · Clinical and translational medicine 2024 · PMID 39440467 · doi:10.1002/ctm2.70072
This dataset
Open GSE266308 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 GSE266308_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: 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 PRJNA1106533 and SRA study SRP505058. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39440467) ↗
Study design
4 × ATAC temporal neocortex, epileptogenic, vs 4 × RNA temporal neocortex, epileptogenic, vs 3 × ATAC temporal neocortex, nonepileptic, vs 3 × RNA temporal neocortex, nonepileptic,

Supports a between-group comparison across 14 samples.

How we read this: 4 replicated groups read from 14 sample titles; they account for 14 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.

Samples in this study
Datasets on a similar topic

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