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| Home > Publications Database > Dataset: snRNA data of Brain section from Parkinson Mouse Model based on inducible expression of human a-syn constructs, v1 |
| Home > Publications Database > Dataset: snRNA data of Brain section from Parkinson Mouse Model based on inducible expression of human a-syn constructs, v1 |
| Dataset | DZNE-2025-00835 |
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2025
Zenodo
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Please use a persistent id in citations: doi:10.5281/zenodo.14893737 doi:10.5281/ZENODO.14893737 doi:10.5281/zenodo.14893736
Abstract: Using 6-months, 16-months, and 24-months old mice of a inducible expression of human a-syn constructs based Parkinson mouse model, we produced a single nucleus RNA dataset by cutting 0mm Bregma to -5mm Bregma. The Chromium 3’ Single Cell Library Kit (10x Genomics) was used and Sequencing was performed on a NovaSeq 6000. Paired 150bp snRNA-seq was performed using the 10X Genomics Gene Expression (GEX) 3´protocol with an NovaSeq 6000 sequencer. For the alignment of reads, a custom reference was created by adding the sequences of the S1/S2 transgene and the CamkIIa promoter to the mm10 mouse reference genome. Count matrices were obtained using the cellranger count 7.1 pipeline, including introns. Six samples were mapped using the bwUni2.0 High-Performance Computing infrastructure. The unfiltered count matrices were loaded into R and corrected for ambient mRNA using SoupX 1.6.0 with default settings, adjusting “tfidfMin” settings between 0.9 and 1.3 depending on the sample. Seurat objects were created for each sample and subsequently merged. Cells were filtered out based on the following criteria: number of unique molecular identifiers (nUMI) 3%, ribosomal gene percentage > 1.5%, or log10(Genes/nUMI)
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