Structural basis for the specificity of PPM1H phosphatase for Rab GTPases
By Michelle onPublished: LRRK2 acts by adding a phosphate group to enzymes known as Rab GTPases, which causes new biological events. The authors analyzed the structure of an enzyme, PPM1H, that counteracts LRRK2 by removing the phosphate group it adds to Rab GTPases. View original preprint.
powereQTL – An R package for calculating sample size and power of bulk tissue and single-cell eQTL analysis
By Blythe Lloyd onPower and sample size calculation for bulk tissue and single-cell eQTL analysis based on ANOVA, simple linear regression, or linear mixed-effects model. It can also calculate power/sample size for testing the association of an SNP to a continuous type phenotype.
HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads. Dataset
By Michelle onDataset associated with DOI: 10.7554/eLife.73971 View preprint.
Software for analyzing the expression of TEs at locus-specific resolution
By Blythe Lloyd onTElocal takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements.
TBK1 knockdown and rescue in Hela-M cells
By Blythe Lloyd onThis protocol transiently depletes TBK1 from HeLa cells and re-introduces a tagged TBK1 along with other relevant components of mitophagy. Because TBK1 is integral in many cellular processes, cells depleted of TBK1 exhibit poor health. Our protocol accomplishes ~70% depletion of endogenous TBK1 within 24 hours without excessive cell death.
VPS13D DNA plasmid generation
By Blythe Lloyd onThis protocol describes the basic molecular cloning technique utilized for the generation of VPS13D constructs in VPS13D bridges the ER to mitochondria and peroxisomes via Miro. This protocol and the enzymes included in it are commercialized by Takara Bio.
LRRK2 at Striatal Synapses: Cell-Type Specificity and Mechanistic Insights
By Blythe Lloyd onReview: This review focuses on pathogenic LRRK2 mutations and their effects on striatial neurons.
Mass spectrometry proteomic data supporting the PPM1H/Rab8A crosslinking study described in doi: 10.15252/embr.202152675
By Michelle onRaw data associated with DOI: 10.15252/embr.202152675