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Glial cell diversity and methamphetamine-induced neuroinflammation in human cerebral organoids

GSE286054 Homo sapiens (human) Single-cell RNA-seq 14 samples Submitted 2025/01/07 Platform GPL20301
At a glance

Single-cell RNA-seq · human · 14 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
14 samples: 5 × 30D Cortical organoid, untreated, batch 2, sample vs 3 × 30D Cortical organoid, untreated, batch 1, sample vs 3 × 30D Cortical organoid, meth-treated, batch 1, sample vs 3 × 30D cortical organoid, meth-treated, batch 2, sampleGroups 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
Glial cell diversity and methamphetamine-induced neuroinflammation in human cerebral organoidsMolecular psychiatry · 2021
Summary (written by the submitters)
Methamphetamine (METH) is a potent stimulant that induces a euphoric state but also causes cognitive impairment, neurotoxicity and neurodevelopmental deficits. Yet, the molecular mechanisms by which METH causes neurodevelopmental defects have remained elusive. Here we utilized human cerebral organoids and single-cell RNA sequencing (scRNA-seq) to study the effects of prenatal METH exposure on fetal brain development. Findings have been reported in Dang et al. 2021, Molecular Psychiatry.
Published in
Glial cell diversity and methamphetamine-induced neuroinflammation in human cerebral organoids
Dang J, Tiwari SK, Agrawal K et al. · Molecular psychiatry 2021 · PMID 32051547 · doi:10.1038/s41380-020-0676-x
This dataset
Open GSE286054 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 GSE286054_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 PRJNA1207551 and SRA study SRP555835. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 32051547) ↗
Study design
5 × 30D Cortical organoid, untreated, batch 2, sample vs 3 × 30D Cortical organoid, untreated, batch 1, sample vs 3 × 30D Cortical organoid, meth-treated, batch 1, sample vs 3 × 30D cortical organoid, meth-treated, batch 2, sample

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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