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BioProject

KAP240761

BioProject Title

Single-cell and spatial transcriptomic analysis to elucidate the molecular mechanisms underlying sporadic Parkinson's disease in South Korea

The heterogeneity in various aspects of Parkinson's disease (PD) is increasingly recognized as an important aspect in understanding the condition, with ethnicity and race being one of the major causes of heterogeneity that affects the risk and symptoms of PD onset. While there have been numerous reports related to PD in East Asia, there has been a lack of contribution from single-cell (or nucleus) transcriptome studies, which have been making significant contributions to understanding PD. In this study, we profiled nuclei extracted from the substantia nigra (SN) of confirmed pathological PD and control patients in South Korea, revealing 8 different cell types through cluster analysis. Monocle-based pseudotime analysis identified two disease-associated trajectories for each astrocyte and microglia and identified genes that differentiate them. Interestingly, we uncovered the inflammatory intervention in the early PD-associated transition in microglia and identified the molecular features of this intermediate state of microglia. In addition, gene regulatory networks (GRNs) based on TENET analysis revealed the detrimental effect of an HSPA5-led module in microglia and MSRB3- and HDAC8- led modules specifying the two different astrocyte trajectories. In SN neurons, we observed high heterogeneity and population changes, a decrease in dopaminergic and glutamatergic neurons and a proportional increase in GABAergic neurons. By deconvolution in spatial transcriptome obtained the PD sample, we confirmed spatiotemporal heterogeneity of neuronal subpopulations and PD-associated progressive gliosis specific to dopaminergic nuclei, SN and ventral tegmental areas (VTAs). In conclusion, our approach has enabled us to identify the genetic and spatial characterization of neurons and to demonstrate different glial fates in PD. These findings advance our molecular understanding of cell type-specific changes in Korean PD progression, providing an important foundation for predicting and validating interventions or drug effects for future treatments.

Common Fields

Common Fields - BioProject, Strategy, Source, Selection, Layout, Instrument, Submission date, Experiments
BioProject	KAP240761
Strategy	RNA-Seq
Source	TRANSCRIPTOMIC SINGLE CELL , TRANSCRIPTOMIC
Selection	cDNA , other , Oligo-dT
Layout	paired
Instrument	HiSeq X Ten
Submission date	2024-07-03
Experiments	14

Accession

Accession - RUNs, BIOSAMPLEs
Runs	All runs [14]
BioSamples	All samples [13]

Experiment Metadata

(14 cases)

Experiment Metadata - SUBMISSION ID, EXPERIMENT ID, Identifier, BIOSAMPLE ID, SAMPLE NAME, LIBRARY IDENTIFIER, TITLE, LIBRARY STRATEGY, LIBRARY SOURCE, LIBRARY SELETION, LIBRARY IAYOUT, FLATFORM, INSTRUMENT MODEL
EXPERIMENT ID	BIOSAMPLE ID	sample_name	library_name	title	library_strategy	library_source	library_selection	library_layout	platform	instrument_model	library_construction_protocol	Submission dateSubmission date	Registration date
KAE24093007	KAS24117480	SNU17	BB24-10-SN17-B	HiSeq X Ten paired-end Sequencing of SNU17	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	paired	ILLUMINA	HiSeq X Ten	Spatial gene expression libraries were prepared using the Visium Spatial Gene Expression v2 protocol according to the manufacturer’s instructions. Tissue sections were placed onto spatially barcoded capture areas, and RNA was released and reverse transcribed to generate spatially barcoded cDNA. The resulting cDNA was amplified and processed to construct sequencing-ready libraries. Final libraries were sequenced on the Illumina HiSeq X Ten platform following standard Illumina sequencing procedures.	2025-05-27	2025-05-21
KAE24093006	KAS24117479	SNU16	BB24-09-SN16-A	HiSeq X Ten paired-end Sequencing of SNU16	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	paired	ILLUMINA	HiSeq X Ten	Spatial gene expression libraries were prepared using the Visium Spatial Gene Expression v2 protocol according to the manufacturer’s instructions. Tissue sections were placed onto spatially barcoded capture areas, and RNA was released and reverse transcribed to generate spatially barcoded cDNA. The resulting cDNA was amplified and processed to construct sequencing-ready libraries. Final libraries were sequenced on the Illumina HiSeq X Ten platform following standard Illumina sequencing procedures.	2025-05-27	2025-05-21
KAE24093005	KAS24117478	SNU14	BB22-25-SN14-B	HiSeq X Ten paired-end Sequencing of SNU14	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	paired	ILLUMINA	HiSeq X Ten	Spatial gene expression libraries were prepared using the Visium Spatial Gene Expression v2 protocol according to the manufacturer’s instructions. Tissue sections were placed onto spatially barcoded capture areas, and RNA was released and reverse transcribed to generate spatially barcoded cDNA. The resulting cDNA was amplified and processed to construct sequencing-ready libraries. Final libraries were sequenced on the Illumina HiSeq X Ten platform following standard Illumina sequencing procedures.	2025-05-27	2025-05-21
KAE24093004	KAS24117477	SNU13_Dup	BB22-11-SN13-A	HiSeq X Ten paired-end Sequencing of SNU13_Dup	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	paired	ILLUMINA	HiSeq X Ten	Spatial gene expression libraries were prepared using the Visium Spatial Gene Expression v2 protocol according to the manufacturer’s instructions. Tissue sections were placed onto spatially barcoded capture areas, and RNA was released and reverse transcribed to generate spatially barcoded cDNA. The resulting cDNA was amplified and processed to construct sequencing-ready libraries. Final libraries were sequenced on the Illumina HiSeq X Ten platform following standard Illumina sequencing procedures.	2025-05-27	2025-05-20
KAE24064930	KAS24091971	SNU13	BB22-11-SN13-D1	HiSeq X Ten paired-end Sequencing of SNU13	RNA-Seq	TRANSCRIPTOMIC	other	paired	ILLUMINA	HiSeq X Ten	Spatial gene expression libraries were prepared using the Visium Spatial Gene Expression v2 protocol according to the manufacturer’s instructions. Tissue sections were placed onto spatially barcoded capture areas, and RNA was released and reverse transcribed to generate spatially barcoded cDNA. The resulting cDNA was amplified and processed to construct sequencing-ready libraries. Final libraries were sequenced on the Illumina HiSeq X Ten platform following standard Illumina sequencing procedures.	2024-07-03	2024-07-01
KAE24064929	KAS24091971	SNU13	BB22-11-SN13-A1	HiSeq X Ten paired-end Sequencing of SNU13	RNA-Seq	TRANSCRIPTOMIC	other	paired	ILLUMINA	HiSeq X Ten	Spatial gene expression libraries were prepared using the Visium Spatial Gene Expression v2 protocol according to the manufacturer’s instructions. Tissue sections were placed onto spatially barcoded capture areas, and RNA was released and reverse transcribed to generate spatially barcoded cDNA. The resulting cDNA was amplified and processed to construct sequencing-ready libraries. Final libraries were sequenced on the Illumina HiSeq X Ten platform following standard Illumina sequencing procedures.	2024-07-03	2024-07-01
KAE24064928	KAS24091970	SNU12	BB19-05-SN12	HiSeq X Ten paired-end Sequencing of SNU12	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	paired	ILLUMINA	HiSeq X Ten	Chromium Next GEM Single Cell 3ʹ Kit v3.1 (dual index)	2024-07-03	2024-07-01
KAE24064927	KAS24091969	SNU11	BB18-10-SN11	HiSeq X Ten paired-end Sequencing of SNU11	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	paired	ILLUMINA	HiSeq X Ten	Chromium Next GEM Single Cell 3ʹ Kit v3.1 (dual index)	2024-07-03	2024-07-01
KAE24064926	KAS24091968	SNU10	BB18-17-SN10	HiSeq X Ten paired-end Sequencing of SNU10	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	paired	ILLUMINA	HiSeq X Ten	Chromium Next GEM Single Cell 3ʹ Kit v3.1 (dual index)	2024-07-03	2024-07-01
KAE24064925	KAS24091967	SNU9	BB18-18-SN9	HiSeq X Ten paired-end Sequencing of SNU9	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	paired	ILLUMINA	HiSeq X Ten	Chromium Next GEM Single Cell 3ʹ Kit v3.1 (dual index)	2024-07-03	2024-07-01
KAE24064924	KAS24091966	SNU8	BB20-13-SN8	HiSeq X Ten paired-end Sequencing of SNU8	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	paired	ILLUMINA	HiSeq X Ten	Chromium Next GEM Single Cell 3ʹ Kit v3.1 (dual index)	2024-07-03	2024-07-01
KAE24064923	KAS24091965	SNU5	BB19-23-SN5	HiSeq X Ten paired-end Sequencing of SNU5	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	paired	ILLUMINA	HiSeq X Ten	Chromium Next GEM Single Cell 3ʹ Kit v3.1 (dual index)	2024-07-03	2024-07-01
KAE24064922	KAS24091964	SNU2	BB19-14-SN2	HiSeq X Ten paired-end Sequencing of SNU2	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	paired	ILLUMINA	HiSeq X Ten	Chromium Next GEM Single Cell 3ʹ Kit v3.1 (dual index)	2024-07-03	2024-07-01
KAE24064921	KAS24091963	SNU1	BB20-9-SN1	HiSeq X Ten paired-end Sequencing of SNU1	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	Oligo-dT	paired	ILLUMINA	HiSeq X Ten	Chromium Next GEM Single Cell 3ʹ Kit v3.1 (dual index)	2024-07-03	2024-07-01

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