ASAP Research Round-Up | Q3 2025
In this second edition of the ASAP Research Round-Up, ASAP shares advancements in Q2 2025 across the ASAP portfolio that fill critical knowledge gaps, promote rapid dissemination of scientific insights, expand resource accessibility, and support the next generation of Parkinson’s researchers.
Gene expression profile at single cell levels of the cells from the controls and tau P251L Drosophila brain
By onTau protein's role in Alzheimer's disease was studied by introducing a human tau mutation into Drosophila using CRISPR. Single-cell RNA sequencing helped identify genes and pathways involved in tauopathy.
scAlleleExpression: R package for downstream analysis of allele specific expression single cell data
By onAn R package for investigating Cell Type specific regulatory genetics using single cell or nuclei allele specific expression data. It loads ASE pipeline output, performs ASE analysis, and works with various ASE pipelines.
scASE_py: Python pacakge for loading single cell allele specific data
By onPython package for single cell allele-specific expression (ASE) output manipulation available at https://github.com/seanken/ASE_pipeline. R package for downstream analysis at https://github.com/seanken/scAlleleExpression.
CellLevel_QC: Extracting cell level QC metrics from CellRanger barcoded bams
By onJava code in this repository retrieves cell level mapping data (intronic reads, intergenic reads, multimapped reads, etc) from CellRanger output. Compatible with CellRanger v5 and v6, may work with newer versions and Spaceranger output.
Single cell allele specific expression processing pipeline for long read data
By onPipeline processes long read single cell/nucleus 10X data (ONT, PacBio, MAS-Seq) to generate gene/isoform-level allele-specific expression (ASE) counts.
ASAP Parkinson Cell Atlas in 5D (PD5D)
By onThe PD5D Atlas deciphers Parkinson's disease molecular blueprint using brain space, disease stage, and cell types dimensions. It includes various omics data and clinical scales to analyze PD progression from healthy aging to Lewy body neuropathology.
Analyses of metabolite profiling of Drosophila Parkinson’s Disease model for identifying novel glial-based therapeutic targets
By onGenetic screening and metabolomics show glial adenosine metabolism as a potential treatment for Parkinson’s disease. Analysis includes measuring metabolite levels in synuclein expressing/control fly brains with different methods.
Developing Allelic Imbalance Analysis from Single-Nucleus RNA-Seq Data
By onAllele-specific expression (ASE) analysis in single-nucleus RNA-seq (snRNA-Seq) helps study genetic variation impact on RNA expression. Experimental and computational choices can enhance ASE analysis results.
HYX990205/ReRx: Drug Repurposing for Parkinson’s Disease
By onToolkit for drug repurposing analysis used in the preprint: "Drug Repurposing for Parkinson's Disease: A Large-Scale Multi-Cohort Study" Find more at https://doi.org/10.1101/2025.05.20.25327943.
TheDongLab/EVscope: v1.0.0
By onEVscope is a tool for analyzing extracellular vesicle RNA sequencing data, addressing challenges like low yield and contamination. It includes quality control, alignment, circular RNA detection, expression quantification, and reporting.
Ventral midbrain dopaminergic (mDA) Neuron Differentiation Protocol
By onOptimized protocol for generating authentic ventral midbrain dopaminergic neurons from human iPSCs enhances cell therapy and modeling, improves consistency across lines, and supports integration with organoid and assembloid systems.
Formation of ventral midbrain Assembloid/Organoids
By onThis pilot establishes brain organoids from iPSC-derived vmDA neurons, optimizing growth conditions and exploring tri-culture integration with microglia to model neurodevelopment and cell-type interactions.
Protocol selection for Saurat et al. CSC 2024 V.2
By onProtocol collection for the study "Genome-wide CRISPR screen reveals neddylation's role in neuronal aging and AD neurodegeneration" by Saurat et al. in Cell Stem Cell 2024. Contains 20 protocols. Full manuscript: DOI: 10.1016/j.stem.2024.06.001.
Protocol selection for Kim et al. Cell 2024 V.2
By onKim et al. in Cell 2024 published "TNF-NF-kB-p53 axis restricts in vivo survival of hPSC-derived dopamine neurons" with 13 protocols. Full text at (https://doi.org/10.1016/j.cell.2024.05.030).
A Novel α-Synuclein K58N Missense Variant in a Patient with Parkinson’s Disease
By on15% of cases of PD are linked to mutations in the SNCA gene. A novel K58N mutation in a patient showed typical PD symptoms, genetic testing, and biophysical studies revealing structural effects and abnormal cellular behavior of SNCA.
Bulk RNAseq of microglia in vitro cultures
By onBulk 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
By onBulk 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
By onStep-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
By onThis 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.
