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 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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Program
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CRN Team Name
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Theme
Protocol 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.
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.
Single-nucleus RNA (snRNA) sequencing
Step-by-step protocol describing the snRNA sequencing workflow for nuclei isolated from post-mortem human brain tissue.
Image resources (Garza et al. 2026)
Brightfield, Immunofluorescent images of KOLF2.1-derived microglia (MGlia) and RC17 hES cells derived dopaminergic neurons by Garza et al (2026).
iPSC QC (Garza et al, 2026)
Quality control reporting table and imaging files for hiPSCs and hESCs lines used in Garza et al., 2026.
TEsingle Software
Software to analyze TE expression in single cell/single nuclei RNA-seq datasets.
TEsingle pipeline for analysis of Martirosyan dataset
Code to analyze Martirosyan et al. substantia nigra single nuclei RNA-seq dataset with TEsingle.
TEsingle benchmarking pipeline
Code to perform benchmarking of simulated single cell/nuclei RNA-seq datasets with TEsingle and other scRNA-seq software.
Simulation data for TEsingle benchmarking
This dataset includes files for benchmarking analysis with TEsingle and other snRNA tools, facilitating reproducibility.
Release Notes – ASAP CRN Cloud – Version 4.0.0
ASAP CRN Cloud released version 4.0.0 with expanded datasets including Human Postmortem-derived Brain Sequencing and Mouse datasets. New collections and individual datasets were added, enhancing PMDBS and Mouse RNA sequencing data.
TEsingle enables locus-specific transposable element expression analysis at single-cell resolution
TEsingle is a tool for analyzing transposable elements (TE) and gene expression in single-cell data. The tool reveals cell-type specific TE expression in Parkinson's Disease patients' brain tissues.
Iso-Seq mapping to L1HS/PA2 consensus sequence
The protocol describes the steps to map HiFi reads to a consensus sequence and retrieve density plots.
Single cell/nuclei RNAseq analysis
This protocol describes the process for the single cell/nuclei RNA sequencing data of the manuscript “L1retrotransposons drive human neuronal transcriptome complexity and functional diversification ” from fetal forebrain and adult…
Microglia differentiation from human pluripotent stem cells
Microglia are crucial for brain development and maintaining homeostasis. They are involved in neurodegenerative diseases and can be generated from human stem cells using established protocols.
L1 retrotransposons drive human neuronal transcriptome complexity and functional diversification
The genetic mechanisms underlying the expansion in size and complexity of the human brain remains poorly understood. L1 retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological…
