GEO series

Dissecting the transcriptome of Parkin (PRKN)-linked Parkinson’s disease using 2D and 3D hiPSC-neuronal models

GSE282152 Homo sapiens (human) RNA-seq (gene expression) 84 samples Submitted 2026/07/20 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 84 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: 84 samples: 28 conditions, mostly in triplicateGroups 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.

Summary (written by the submitters)

Mutations in the Parkin (PRKN) gene are the most common known cause of autosomal recessive early-onset Parkinson’s disease (PD), and Parkin dysfunction represents a risk factor for idiopathic PD. Parkin is an E3 ubiquitin ligase, involved in protein quality control and the removal of damaged mitochondria. Here, we generate human induced pluripotent stem cell (hiPSC)-derived midbrain dopaminergic neurons using both a 2D differentiation protocol and our recently developed 3D method based on the microencapsulation of hiPSCs in small alginate/fibronectin beads.

Read the full summary ↓

The transcriptional signature of cells from PD patients carrying PRKN mutations is evaluated at the neuronal stage and during the differentiation process. Analyses of mutation-specific gene sets and associated pathways reveal multiple biological processes implicated in PRKN-pathology, including synaptic and metabolic function, inflammation, and intracellular trafficking, reflecting a layered disease development. These data map the contribution of Parkin in early PD pathogenesis and progression before overt neurodegeneration.

This dataset

Open GSE282152 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 GSE282152_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 PRJNA1187473 and SRA study SRP545844. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

28 conditions, mostly in triplicate

2011 cells,2D,D10,mut, ×3 2011 cells,2D,D20,mut, ×3 2011 cells,2D,D35,mut, ×3 802 cells,2D,D10,ctrl, ×3 802 cells,2D,D20,ctrl, ×3 802 cells,2D,D35,ctrl, ×3 B125 cells,2D,D10,mut, ×3 B125 cells,2D,D20,mut, ×3 +20 more

Supports a between-group comparison across 84 samples.

How we read this: 28 replicated groups read from 84 sample titles; they account for 84 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

GSM8636847 2011 cells,2D,D10,mut,rep1 2011 cells,2D,D10,mut,
GSM8636848 2011 cells,2D,D10,mut,rep2 2011 cells,2D,D10,mut,
GSM8636849 2011 cells,2D,D10,mut,rep3 2011 cells,2D,D10,mut,
GSM8636850 2011 cells,2D,D20,mut,rep1 2011 cells,2D,D20,mut,
GSM8636851 2011 cells,2D,D20,mut,rep2 2011 cells,2D,D20,mut,
GSM8636852 2011 cells,2D,D20,mut,rep3 2011 cells,2D,D20,mut,
GSM8636853 2011 cells,2D,D35,mut,rep1 2011 cells,2D,D35,mut,
GSM8636854 2011 cells,2D,D35,mut,rep2 2011 cells,2D,D35,mut,
GSM8636855 2011 cells,2D,D35,mut,rep3 2011 cells,2D,D35,mut,
GSM8636856 802 cells,2D,D10,ctrl,rep1 802 cells,2D,D10,ctrl,
GSM8636857 802 cells,2D,D10,ctrl,rep2 802 cells,2D,D10,ctrl,
GSM8636858 802 cells,2D,D10,ctrl,rep3 802 cells,2D,D10,ctrl,
GSM8636859 802 cells,2D,D20,ctrl,rep1 802 cells,2D,D20,ctrl,
GSM8636860 802 cells,2D,D20,ctrl,rep2 802 cells,2D,D20,ctrl,
GSM8636861 802 cells,2D,D20,ctrl,rep3 802 cells,2D,D20,ctrl,
GSM8636862 802 cells,2D,D35,ctrl,rep1 802 cells,2D,D35,ctrl,
GSM8636863 802 cells,2D,D35,ctrl,rep2 802 cells,2D,D35,ctrl,
GSM8636864 802 cells,2D,D35,ctrl,rep3 802 cells,2D,D35,ctrl,
GSM8636865 B125 cells,2D,D10,mut,rep1 B125 cells,2D,D10,mut,
GSM8636866 B125 cells,2D,D10,mut,rep2 B125 cells,2D,D10,mut,
GSM8636867 B125 cells,2D,D10,mut,rep3 B125 cells,2D,D10,mut,
GSM8636868 B125 cells,2D,D20,mut,rep1 B125 cells,2D,D20,mut,
GSM8636869 B125 cells,2D,D20,mut,rep2 B125 cells,2D,D20,mut,
GSM8636870 B125 cells,2D,D20,mut,rep3 B125 cells,2D,D20,mut,
GSM8636871 B125 cells,2D,D35,mut,rep1 B125 cells,2D,D35,mut,
GSM8636872 B125 cells,2D,D35,mut,rep2 B125 cells,2D,D35,mut,
GSM8636873 B125 cells,2D,D35,mut,rep3 B125 cells,2D,D35,mut,
GSM8636874 SFC cells,2D,D10,ctrl,rep1 SFC cells,2D,D10,ctrl,
GSM8636875 SFC cells,2D,D10,ctrl,rep2 SFC cells,2D,D10,ctrl,
GSM8636876 SFC cells,2D,D10,ctrl,rep3 SFC cells,2D,D10,ctrl,
GSM8636877 SFC cells,2D,D20,ctrl,rep1 SFC cells,2D,D20,ctrl,
GSM8636878 SFC cells,2D,D20,ctrl,rep2 SFC cells,2D,D20,ctrl,
GSM8636879 SFC cells,2D,D20,ctrl,rep3 SFC cells,2D,D20,ctrl,
GSM8636880 SFC cells,2D,D35,ctrl,rep1 SFC cells,2D,D35,ctrl,
GSM8636881 SFC cells,2D,D35,ctrl,rep2 SFC cells,2D,D35,ctrl,
GSM8636882 SFC cells,2D,D35,ctrl,rep3 SFC cells,2D,D35,ctrl,
GSM8636883 2011 cells,3D,D10,mut,rep1 2011 cells,3D,D10,mut,
GSM8636884 2011 cells,3D,D10,mut,rep2 2011 cells,3D,D10,mut,
GSM8636885 2011 cells,3D,D10,mut,rep3 2011 cells,3D,D10,mut,
GSM8636886 2011 cells,3D,D20,mut,rep1 2011 cells,3D,D20,mut,

+ 44 more — browse all 84 samples with per-sample file links →

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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.