TY  - CHART
AU  - Lee, Jaehyun
TI  - Dataset: Visium Spatial data of Brain section from Parkinson Mouse Model based on inducible expression of human a-syn constructs: 3-months
PB  - Zenodo
M1  - DZNE-2025-00789
PY  - 2025
AB  - Using 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.
LB  - PUB:(DE-HGF)32
DO  - DOI:10.5281/ZENODO.15274014
UR  - https://pub.dzne.de/record/279462
ER  -