Output 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.
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Output Type
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CRN Team Name
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Bulk RNAseq of microglia in vitro cultures
Bulk RNAseq data of human pluripotent stem cells differentiated into microglia was generated using Illumina TruSeq kit. Cells were induced through mesodermal and myeloid differentiation to produce microglia-like cells, mimicking human microglia.
Bulk RNAseq of dopaminergic neurons in vitro cultures
Bulk RNAseq data of hES and hiPSCs differentiated into dopaminergic neurons from ventral midbrain fate were generated using Illumina TruSeq Stranded mRNA kit. Detailed protocols for differentiation can be found at protocols.io.
Oxford Nanopore Technologies (ONT) direct RNA sequencing
Step-by-step protocol for ONT direct RNA sequencing: RNA extraction, mRNA poly(A) selection, library preparation for ONT direct RNA sequencing, and ONT direct RNA data analysis.
A framework for efficient CRISPRi-mediated silencing of retrotransposons in human pluripotent stem cells
This methods paper outlines silencing transposable elements in hiPSCs using CRISPRi. Describes gRNA design, validation via multiome approach. Enables functional studies on TE transcription in hiPSC models.
Release Notes – ASAP CRN Cloud
Summary: Release notes for version 1.0.0 of CRN Cloud platform, released on June 25, 2024, detailing latest updates and enhancements.
A molecular atlas of cell-type specific signatures in the parkinsonian striatum
Progressive dopamine loss in PD affects striatum cells differently. Transcriptomic analysis in mouse and human models reveals changes in neuronal and glial populations, highlighting resilient and vulnerable cell types for potential new treatments.
Proteomics for STING KO and STINGRRAA RAW 264.7 macrophages
Using immunopeptidomics analysis we showed that STING regulates the repertoire of peptides displayed at the cell surface of macrophages during inflammation, highlighting a potential role in immunosurveillance and potential targets for therapy
Code used in “Lrrk2 G2019S mutation incites increased cell-intrinsic neutrophil effector functions and intestinal inflammation in a model of infectious colitis”
Using scRNAseq and flow cytometry, we demonstrated that the Lrrk2-G2019S mutation is associated with an increased neutrophil presence in the colonic lamina propria, Th17 skewing, upregulated Il17a, and greater colonic pathology during infection.
Transcriptomic analysis of colonic lamina propria cells in LRRK2 G2019S mice compared to wild type following intestinal microbial infection
Using scRNAseq and flow cytometry, we demonstrated that the Lrrk2 G2019S mutation is associated with an increased neutrophil presence in the colonic lamina propria during infection and a Th17 skewing, upregulated Il17a, and greater colonic…
Activation of transposable elements is linked to a region- and cell-type-specific interferon response in Parkinson’s disease
Study explores transposable elements role in Parkinson's disease neuroinflammation. TE activation in specific brain regions correlates with innate immune responses, indicating potential involvement in chronic neuroinflammation and PD progression.
Tailored workflows for the analysis of transposable elements (Garza et al, 2025)
Garza et al. (2025) created customized workflows for transposable element analysis across various data types. Workflows are in Snakemake, Jupyter notebooks, R markdowns, and scripts. Details are in the GitHub README.
Faecalibacterium prausnitzii, depleted in the Parkinson’s disease microbiome, improves motor deficits in α-synuclein overexpressing mice
Treatment with an 8-member consortium of bacteria depleted in PD patients, or the single member F. prausnitzii, improves motor and GI function and reduces αSyn aggregates in the brain of a mouse model of PD.
Motor behavior, GI behavior, protein, and volatile fatty acid assay data and analysis code associated with Moiseyenko et al. 2025
Code and data used for the statistical analysis of motor behavior and gut physiology tests, and downstream protein assays from Moiseyenko et al. (2025)
RNAseq data associated with Moiseyenko et al. 2025
BAM files for RNA sequencing of large intestine of wild-type, Thy1-ASO, and Faecalibacterium prausnitzii-treated Thy1-ASO mice from Moiseyenko et al. (2025)
Data and code for shotgun metagenomics associated with Moiseyenko et al. 2025
Data and scripts to retrieve and analyze shotgun metagenomic data of wild-type, Thy1-ASO, and Faecalibacterium prausnitzii-treated Thy1-ASO mice from Moiseyenko et al. (2025)
