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.
Probedesign pipeline for the inhouse generation of seqFISH probes
The probe design pipeline works by inputting the transcript id’s for which probes have to be designed. Additional probe design parameters such as GC% or melting temperature can be changed via the config file. The pipeline will output the designed probes in fasta format and a csv file with the results of all filtering steps.
Comprehensive structural variant detection: from mosaic to population-level
Preprint: The authors developed Sniffles2, a faster and more accurate method to analyze long-ready structural variation calling. This method also solves the problem of family to population-level SV calling to produce fully genotyped VCF files.
Microfluidic Chip Production v1.1 V.2
Protocol for producing microfluidic chips used in HyDrop experiment.
Step-by-step protocol for execution of HyDrop-ATAC.
Step-by-step protocol for performing HyDrop-RNA. The duration of each step assumes an experienced protocol user. For a first-time user, we recommend doubling the expected time for each step.
Multiple genome alignment in the telomere-to-telomere assembly era
Review: This review provides an overview of the algorithmic template that most multiple genome alignment methods follow. We also discuss prospective areas of improvement of multiple genome alignment for keeping up with continuously arriving high-quality T2T assembled genomes and for unlocking clinically-relevant insights.
More of less: novel multi-ome profiling of single human neurons
Review: Epigenetic modifications to DNA and chromatin interact to influence gene expression and cellular phenotypes, but defining these omics layers in complex tissues is a daunting task. In this issue of Cell Genomics, Luo et al. describe a novel single-cell multi-omic method, simultaneously profiling transcriptome, DNA methylome, and chromatin accessibility, to shed light on human neurons.
Tutorials for HyDrop data analysis
HyDrop Bead Generation & PCR Barcoding v1.0
Protocol for producing dissolvable barcoded hydrogel beads used in HyDrop experiments.
HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads
The data available in this repository can be used to replicate all the figures in the authors’ manuscript using their data analysis tutorial available here: https://github.com/aertslab/hydrop_data_analysis