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Catalog
ASAP is committed to accelerating the pace of discovery and informing a path to a cure for Parkinson’s disease through collaboration, research-enabling resources, and data sharing. We’ve created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.
Article
Splicing accuracy varies across human introns, tissues, and age
This in-depth characterization of mis-splicing can have important implications for our understanding of the role of splicing inaccuracies in human disease and the interpretation of long-read RNA-sequencing data.
Themes
Article
ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2
Published: Parkinson’s disease likely reflects a complex interaction among genetic and environmental factors. Here, the role of nicotine, SV2 and the alpha-synuclein were examined. The study suggests that SV2 may be needed for the protection nicotine provides from Parkinson’s-related neurotoxicity. View original preprint.
Themes
Code
Long-read RNA seq analysis using Talon
This is a snakemake pipeline that takes Oxford Nanopore Sequencing (ONT) data (fastq) as input, generates fastq stats using nanostat, performs fastq processing and filtering using pychopper, maps the reads to the genome using minimap2, and uses talon to assemble and quantify transcripts. It is forked from ANNSeq. The link includes the dag of the pipeline.
Themes
Article
Pseudogenes limit the identification of novel common transcripts generated by their parent genes
Preprint: Genetic analyses are often complicated by genomic sequences with high sequence similarity. Here, the authors examined the role of pseudogenes on transcriptomic analyses using GB1 and GBAP1 as examples.
Themes
Lab Resource
Lentivirus plasmids for sgRNA: pLV[Exp]-U6>NT-Seq1-hPGK>mApple
Plasmid vector encoding a non-targeting sgRNA sequence under a U6 promoter and a mApple fluorescent reporter.
Generated by Vectorbuilder in the pLV[Exp] backbone
Teams
Themes
Code
Splicing-accuracy-manuscript
Code for the splicing-accuracy manuscript (pre-print DOI to follow).
Teams
Themes
Dataset
Time to LiD GWAS dataset
GWAS dataset derived on the study of LiD genetic determinants together with README. Code used to generate this GWAS file can be accessed at https://doi.org/10.5281/zenodo.7794491
Teams
Themes
Protocol
Nuclear isolation of post-mortem brain tissue for snRNAseq
This protocol details how to isolate nuclei from frozen brain tissue for single nuclear RNA sequencing using 10x Genomics GEM isolation using the Chromium accessory and Single Cell 3ʹ Reagent Kits.
Teams
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Article
KAT8 compound inhibition inhibits PINK1/Parkin-dependent mitophagy and initiates mitochondrial delivery to lysosomes
Preprint: The KAT8 gene encodes a lysine acetyltransferase and represents the catalytically active subunit of the non-specific lethal (NSL) epigenetic remodeling complex. The authors’ study provided additional support for KAT8 inhibition as a regulator of mitophagy and autophagy processes.
Teams
Themes
Lab Resource
Lentivirus plasmid: pLV[Exp]-U6>KANSL1_P1_Seq1-hPGK>mApple
Plasmid vector encoding a sgRNA sequence which targets the KANSL1 promoter from CRISPRi, under a U6 promoter and a mApple fluorescent reporter.
Generated by Vectorbuilder in the pLV[Exp] backbone.
Teams
Themes
Lab Resource
Lentivirus plasmid: pLV[Exp]-U6>KAT8_P1_Seq1-hPGK>mApple
Plasmid vector encoding a sgRNA sequence which targets the human KAT8 promoter for CRISPRi, under a U6 promoter and a mApple fluorescent reporter.
Generated by Vectorbuilder in the pLV[Exp] backbone.
Teams
Themes
Lab Resource
“Plasmid vector encoding a sgRNA sequence which targets the human KAT8 promoter for CRISPRi, under a U6 promoter and a mApple fluorescent reporter. Generated by Vectorbuilder in the pLV[Exp] backbone.”
Plasmid vector encoding a sgRNA sequence which targets the human PINK1 promoter for CRISPRi, under a U6 promoter and a mApple fluorescent reporter.
Generated by Vectorbuilder in the pLV[Exp] backbone.
Teams
Themes
Article
The Emerging Role of LRRK2 in Tauopathies
Review: Authors review the emerging evidence and discuss the potential impact of LRRK2 dysfunction on tau aggregation, lysosomal function, and endocytosis and exocytosis.
Teams
Themes
Protocol
LRRK2 Immunofluorescent staining
Protocol for immunofluorescent staining for LRRK2 in cultured cells using the MJFF2 (c41-2) antibody.
Teams
Themes