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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.
Report
README guide for code
The purpose of this document is to provide guidance on how to write README files for code.
Dataset
Human Postmortem-Derived Brain Sequencing Collection (Harmonized Collection)
The Human Postmortem-Derived Brain Sequencing Collection is a harmonized repository comprised of sequencing data contributed by ASAP CRN teams.
Article
The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1
Published: 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. View original preprint.
Code
Software for analyzing the expression of TEs at locus-specific resolution
TElocal takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements.
Teams
Article
LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification
Published: CRISPRi-silencing of LINC01876 results in reduced size of cerebral organoids and premature differentiation of neural progenitors, implicating L1s in human-specific developmental processes. In summary, the authors’ results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain. View original preprint.
Teams
Protocol
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 prefrontal cortex tissue.
Teams
Protocol
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.
Teams
Protocol
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.
Teams
Protocol
Bulk RNA sequencing analysis
This protocol describes the steps for the bioinformatical analysis of bulk RNA sequencing with a focus on evolutionary young L1s.
Teams
Code
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.
Teams