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.

Article

The annotation and function of the Parkinson’s and Gaucher disease-linked gene GBA1 has been concealed by its protein-coding pseudogene GBAP1

Here, 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.

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.

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.

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.

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.

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.

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.