000279462 001__ 279462
000279462 005__ 20250820091642.0
000279462 0247_ $$2doi$$a10.5281/ZENODO.15274014
000279462 0247_ $$2doi$$a10.5281/zenodo.15274013
000279462 037__ $$aDZNE-2025-00789
000279462 1001_ $$0P:(DE-2719)9002103$$aLee, Jaehyun$$b0
000279462 245__ $$aDataset: Visium Spatial data of Brain section from Parkinson Mouse Model based on inducible expression of human a-syn constructs: 3-months
000279462 260__ $$bZenodo$$c2025
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000279462 520__ $$aUsing 3-months old mice of a inducible expression of human a-syn constructs based Parkinson mouse model, we produced a Visium Spatial V1 platform (10x Genomics) data. Sequencing was performed on a NovaSeq 6000 with PE150. Sequences were fiducially aligned to spots using Loupe Browser ver. 8. All aligned sequences were mapped using spaceranger count 3.0.1 with a custom refence, which included sequences for the promotor and transgene (Camk2aTTA, V1S/SV2) to the mouse genome mm39. We filtered each sample of the Visium Spatial dataset based on the MAD filtering of number of reads (nUMI), number of genes (nGene), and percentage of mitochondrial genes (percent.mt). A spot was filtered out if it was outside of 3x MAD value in at least two metrics. Filtered samples were merged into one Seurat 5.1.0 object and we obtained normalized counts by the SCTransform function of Seurat. Integration was performed using Harmony 1.2.0 on 50 PCA embeddings and clustering was done using Leiden clustering based on 30 harmony embeddings. Integrated clusters were visualized using the UMAP method. Samples that were not successfully integrated (based on similarity measures of the harmony embeddings) and showed high percentage.mt or low nUMI levels compared to other samples, were removed from subsequent analysis. A final integration and clustering were performed after filtering. Regions were first annotated based on a 0.1 resolution clustering to get high level region annotation (Cortex, Hippocampus, Subcortex). Each high-level region was further annotated based on either more granular resolutions or subclustering. Marker genes from mousebrain.org and literature were used in combination with the Allen mouse brain atlas to obtain anatomically relevant annotations.
000279462 536__ $$0G:(DE-HGF)POF4-352$$a352 - Disease Mechanisms (POF4-352)$$cPOF4-352$$fPOF IV$$x0
000279462 588__ $$aDataset connected to DataCite
000279462 7001_ $$0P:(DE-2719)9001513$$aDanzer, Karin$$b1$$eProject Leader
000279462 773__ $$a10.5281/ZENODO.15274014
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000279462 9101_ $$0I:(DE-588)1065079516$$6P:(DE-2719)9002103$$aDeutsches Zentrum für Neurodegenerative Erkrankungen$$b0$$kDZNE
000279462 9101_ $$0I:(DE-588)1065079516$$6P:(DE-2719)9001513$$aDeutsches Zentrum für Neurodegenerative Erkrankungen$$b1$$kDZNE
000279462 9141_ $$y2025
000279462 9131_ $$0G:(DE-HGF)POF4-352$$1G:(DE-HGF)POF4-350$$2G:(DE-HGF)POF4-300$$3G:(DE-HGF)POF4$$4G:(DE-HGF)POF$$aDE-HGF$$bGesundheit$$lNeurodegenerative Diseases$$vDisease Mechanisms$$x0
000279462 9201_ $$0I:(DE-2719)5000072$$kAG Danzer$$lMechanisms of Propagation$$x0
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