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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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 – 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…
Bulk RNA sequencing analysis
This protocol describes the steps for the bioinformatical analysis of bulk RNA sequencing with a focus on evolutionary young L1s.
The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1
The authors identify novel transcripts from both GBA1 and GBAP1, including protein-coding transcripts that are translated in vitro and detected in proteomic data, but that lack GCase activity.
Genome-wide determinants of mortality and motor progression in Parkinson’s disease
The authors examined the impact of gene variants on mortality and cognitive impairment in PD. Only the non-Gaucher disease causing GBA PD risk variant E326K, of the known PD risk variants, was associated with progression in PD.
Isolation of NeuN+ cells from brain tissue (for CUT and RUN)
This protocol describes the steps to isolate NeuN+ cells from brain tissue in preparation for CUT and RUN.
Software for analyzing the expression of TEs at locus-specific resolution
We enable the locus-specific analysis of transposable elements, with curated GTF files to improve detection of yound transposable elements, such as HERVs and young L1s. Parts of this software will be used for single-cell TE anlaysis protocols, which…
LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification
The genetic mechanisms underlying the expansion in size and complexity of the human brain remain poorly understood. Long interspersed nuclear element–1 (L1) retrotransposons are a source of divergent genetic information in hominoid genomes, but…
ASAP CRN Cloud Release Notes – Version 3.0.0
Summary: Release notes for version 3.0.0 of CRN Cloud platform, released on September 30, 2025, detailing latest updates and enhancements.
Scripts for snRNAseq data analysis
Scripts for analyzing single nuclei sequencing data from healthy and Parkinson's Disease brains include creating a reference database with transposable element annotations and a file for Cell Ranger to produce snRNA count matrices.
