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Effect of GBA1 deficiency in human iPSC-derived dopaminergic neurons and astrocytes

GSE315738 Homo sapiens (human) RNA-seq (gene expression) 54 samples Submitted 2026/01/10 Platform GPL34284
At a glance

RNA-seq (gene expression) · human · 54 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
54 samples: 18 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 gene glucosidase, beta acid 1 (GBA1) are the strongest genetic risk factor for Parkinson’s disease (PD) and associate with faster disease progression. GBA1 is expressed in all cell types of the central nervous system, with some evidence supporting higher expression in glial cells than neurons.
Read the full summary ↓
To elucidate possible divergent functions in neurons versus glia, we differentiated human iPSCs generated from an individual with PD heterozygous for the GBA1 pathogenic null variant IVS2+1 (GBA1IVS/+),Mutations in the gene glucosidase, beta acid 1 (GBA1) are the strongest genetic risk factor for Parkinson’s disease (PD) and associate with faster disease progression. GBA1 is expressed in all cell types of the central nervous system, with some evidence supporting higher expression in glial cells than neurons. To elucidate possible divergent functions in neurons versus glia, we generated human iPSCs from fibroblasts from an individual with PD carrying the GBA1 c.115+1 G>A, also known as IVS2+1 G>A variant (GBA1IVS/+). This intronic GBA1 variant is associated with severe neuronopathic Gaucher’s disease and interrupts the canonical splice site following exon 2, leading to nonsense mediated decay and is therefore considered a null allele. An isogenic GBA1+/+ Rev control was generated by CRISPR/Cas9 genome editing to revert the GBA1 IVS2+1 G>A variant back to wildtype, and in the genome editing process, an iPSC clone homozygous for GBA1 IVS2+1 G>A was also generated (GBA1IVS/IVS). A matched control iPSC clone that remained unedited after CRISPR/Cas9 genome editing, maintaining heterozygosity for GBA1 IVS2+1 G>A, was also isolated (GBA1IVS/+ A4).Transcriptomic analysis of GBA1-deficient neurons and astrocytes revealed cell-type specific profiles. GBA1deficiency in neurons downregulated genes associated with immune response and upregulation of cholesterol synthesis, while GBA1 deficiency in astrocytes downregulated genes associated with translation and upregulated genes involved in extracellular matrix biogenesis, suggestive of gliosis. The transcriptomic profile of GBA1-deficient astrocytes was consistent with neurotoxic reactive astrocytes. Together, these findings indicate that GBA1deficiency has cell type-specific effects, where neurons have increased vulnerability to alterations in endolysosomal trafficking leading to α-synucleinopathy while GBA1 deficiency in astrocytes leads to increased neurotoxic reactivity but not impairment in endolysosomal trafficking and development of a-synuclein pathology.
This dataset
Open GSE315738 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 GSE315738_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 PRJNA1398870 and SRA study SRP660051. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
18 conditions, mostly in triplicate
Control-clone1-astrocytes ×3 Control-clone1-neurons ×3 Control-clone2-astrocytes ×3 Control-clone3-astrocytes ×3 Control-clone3-neurons ×3 GBA IVS/+-clone1-astrocytes ×3 GBA IVS/+-clone1-neurons ×3 GBA IVS/+-clone2-astrocytes ×3 +10 more

Supports a between-group comparison across 54 samples.

How we read this: 18 replicated groups read from 54 sample titles; they account for 54 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

+ 14 more — browse all 54 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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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.