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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ASAP CRN Cloud Release Notes – 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 harmonized collections and individual datasets were added, enhancing research possibilities.
ASAP CRN Cloud Release Notes – Version 2.0.0
Version: 2.0.0 Release Date: December 11, 2024 This release notes document provides a concise overview of the updates and enhancements introduced in Version 2.0.0 of the CRN Cloud platform.
ASAP CRN Cloud Release Notes – Version 1.0.0
Version: 1.0.0 Release Date: June 25, 2024 This release notes document provides a concise overview of the updates and enhancements introduced in Version 1.0.0 of the CRN Cloud platform.
ASAP CRN Cloud Release Notes – Version 1.0.0-beta
Version: 1.0.0-beta Release Date: March 6, 2024 This release notes document provides a concise overview of the updates and enhancements introduced in Version 1.0.0-beta of the CRN Cloud platform.
ASAP CRN Cloud Release Notes – Version 0.0.1
Version: 0.0.1 Release Date: November 10, 2023 This release notes document provides a concise overview of Version 0.0.1 of the CRN Cloud platform.
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.
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.
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.
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.
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…
