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Molecular Insights into PCB Neurotoxicity: Comparing Transcriptomic Responses across Dopaminergic Neurons, Population Blood Cells, and Parkinson's Disease Pathology

GSE253569 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2024/08/29 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 24 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
24 samples: 24 × iPSCs dopaGroups 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
Molecular insights into PCB neurotoxicity: Comparing transcriptomic responses across dopaminergic neurons, population blood cells, and Parkinson's disease pathologyEnvironment international · 2024
Summary (written by the submitters)
In this study, we conducted a comprehensive assessment of the transcriptomic responses in iPSC-derived dopaminergic neurons upon exposure to different concentrations (0.01 μM, 0.5 μM, and 10 μM) of PCBs. Specifically, we focused on PCB-180, a congener known for its relatively high accumulation in human brains. The exposure durations were 24 hours and 74 hours, allowing us to capture both short-term and more prolonged effects on gene expression patterns.
Published in
Molecular insights into PCB neurotoxicity: Comparing transcriptomic responses across dopaminergic neurons, population blood cells, and Parkinson's disease pathology
Krauskopf J, Eggermont K, Caiment F et al. · Environment international 2024 · PMID 38608384 · doi:10.1016/j.envint.2024.108642
This dataset
Open GSE253569 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 GSE253569_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 PRJNA1066295 and SRA study SRP484635. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38608384) ↗
Study design
24 × iPSCs dopa

Supports a between-group comparison across 24 samples.

How we read this: 1 replicated groups read from 24 sample titles; they account for 24 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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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.