Web portal (shiney ap) for analysis of total proteomes in response to nutrient stress
By onWeb portal (shiney app) for analysis of total proteomes in response to nutrient stress Associated with preprint: https://doi.org/10.1101/2022.12.06.519342
Code for analysis of ER-phagy in iNeurons via proteomics
By onCode for analysis of ER-phagy in iNeurons via proteomics. Associated with preprint: https://doi.org/10.1101/2023.06.26.546565
pCAG-MBP-Foldon-ATG9 (723-839)
By onPlasmid for expression of ATG9 C-terminal tail trimer in mammalian cells.
Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery
By onDuring autophagy initiation, the curved phagophore is stabilized. Using in vitro reconstitution and MD simulations, authors show that WIPI2 and ATG16L1 bind these curved phagophores and the ATG12-5-16L1 complex is responsible for membrane curvature.
Evaluation of an adapted semi-automated DNA extraction for human salivary shotgun metagenomics
By onThis study demonstrates that the authors’ semi-automated protocol is suitable for shotgun metagenomic analysis.
cDNA clone for bacterial expression of human PPM1H D288A
By onPlasmid for bacterial expression of human PPM1H (D288A); contains TEV protease site for removal of 6His tag.
Proband-NFL Analysis
By onCode used for the manuscript "Combining biomarkers for prognostic modelling of Parkinson’s disease" by Niro Viijaratnam and colleagues.
Protocol for Data Independent Acquisition – Mass spectrometry analysis – a DIA-based Organelle Proteomics
By onHere the authors provide a detailed protocol for the Data Independent Acquisition (DIA)-based mass spectrometry (MS) data acquisition method for proteomic profiling of the Golgi.
H9 ES AAVS1-NGN2 FAM134C/A/B-/-;TEX264-/-; CCPG1-/-
By onES cells were used to create iNeurons lacking ER-phagy receptors FAM134C, A, B, TEX264, and CCPG1. CRISPR/Cas9 was used to introduce a NEUROG2 construct in the AAVS1 locus. Knockouts included CCPG1, RETREG1, RETREG2, RETREG3, and TEX264.
KAT8 compound inhibition inhibits the initial steps of PINK1-dependant mitophagy
By onThe authors provide additional support for KAT8 inhibition as a regulator of mitophagy and autophagy processes.
ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2
By onggtranscript simplifies visualizing transcript structure with new geoms like range(), intron(), junction(), and junction_label_repel(). It extends ggplot2's flexibility to create informative plots for publication.
Microbes and Parkinson’s Disease: from associations to mechanisms
By onSeveral microbes, including viruses, bacteria, and fungi, have been associated with an increased risk of PD in humans. Microbial infections can induce similar common pathways that are associated with PD, including systemic inflammatory responses, α-synuclein misfolding, and disruption of mitochondria. PD-associated gene mutations can impact host–microbe interactions, suggesting that even familial forms of PD may be influenced by microbes.
pLenti HsATP13A3 D498N
By onTransfer plasmid for lenti viral vector production, Expresses D498N mutant of Homo sapiens ATP13A3
MBP Pulldown Assay of ATG9A Truncations
By onProtocol describing MBP Pulldown Assay of ATG9A Truncations.
Lentivirus plasmid: pLV[Exp]-U6>PINK1_P1_Seq3-hPGK>mApple
By onPlasmid: Plasmid vector encoding a sgRNA sequence which targets the human PINK1 promoter for CRISPRi, under a U6 promoter and a mApple fluorescent reporter. Generated by Vectorbuilder in the pLV backbone.
H9 ES AAVS1-NGN2 FAM134C/A/B-/-;TEX264-/-
By onES cells were modified using CRISPR/Cas9 to lack ER-phagy receptor genes FAM134C, A, B, and TEX264. NEUROG2 construct was inserted into the AAVS1 locus. Cells were derived from human embryonic stem cells at the blastocyst stage.
Purification and Crystallization of ATG9 HDIR-ATG101:ATG13 complex
By onPurification and Crystallization of ATG9 HDIR (828-839) fused ATG101 (1-198):ATG13 (1-197).
Purification of the PE2 nCas9-RT protein
By onThis protocol describes the process of expressing and purifying the nicking Cas9-MMLV RT fusion protein for prime editing.
Code for splicing-accuracy-manuscript
By onCode used for manuscript: Splicing accuracy varies across human introns, tissues and age
