TheDongLab/EVscope: v1.0.0
By onEVscope is a tool for analyzing extracellular vesicle RNA sequencing data, addressing challenges like low yield and contamination. It includes quality control, alignment, circular RNA detection, expression quantification, and reporting.
Ventral midbrain dopaminergic (mDA) Neuron Differentiation Protocol
By onOptimized protocol for generating authentic ventral midbrain dopaminergic neurons from human iPSCs enhances cell therapy and modeling, improves consistency across lines, and supports integration with organoid and assembloid systems.
Formation of ventral midbrain Assembloid/Organoids
By onThis pilot establishes brain organoids from iPSC-derived vmDA neurons, optimizing growth conditions and exploring tri-culture integration with microglia to model neurodevelopment and cell-type interactions.
Protocol selection for Saurat et al. CSC 2024 V.2
By onProtocol collection for the study "Genome-wide CRISPR screen reveals neddylation's role in neuronal aging and AD neurodegeneration" by Saurat et al. in Cell Stem Cell 2024. Contains 20 protocols. Full manuscript: DOI: 10.1016/j.stem.2024.06.001.
Protocol selection for Kim et al. Cell 2024 V.2
By onKim et al. in Cell 2024 published "TNF-NF-kB-p53 axis restricts in vivo survival of hPSC-derived dopamine neurons" with 13 protocols. Full text at (https://doi.org/10.1016/j.cell.2024.05.030).
A Novel α-Synuclein K58N Missense Variant in a Patient with Parkinson’s Disease
By on15% of cases of PD are linked to mutations in the SNCA gene. A novel K58N mutation in a patient showed typical PD symptoms, genetic testing, and biophysical studies revealing structural effects and abnormal cellular behavior of SNCA.
Bulk RNAseq of microglia in vitro cultures
By onBulk RNAseq data of human pluripotent stem cells differentiated into microglia was generated using Illumina TruSeq kit. Cells were induced through mesodermal and myeloid differentiation to produce microglia-like cells, mimicking human microglia.
Bulk RNAseq of dopaminergic neurons in vitro cultures
By onBulk RNAseq data of hES and hiPSCs differentiated into dopaminergic neurons from ventral midbrain fate were generated using Illumina TruSeq Stranded mRNA kit. Detailed protocols for differentiation can be found at protocols.io.
Oxford Nanopore Technologies (ONT) direct RNA sequencing
By onStep-by-step protocol for ONT direct RNA sequencing: RNA extraction, mRNA poly(A) selection, library preparation for ONT direct RNA sequencing, and ONT direct RNA data analysis.
A framework for efficient CRISPRi-mediated silencing of retrotransposons in human pluripotent stem cells
By onThis methods paper outlines silencing transposable elements in hiPSCs using CRISPRi. Describes gRNA design, validation via multiome approach. Enables functional studies on TE transcription in hiPSC models.
New Imaging Tech Spots Hidden Protein Predicting Parkinson’s Disease
This news story reports on a new, advanced imaging method that allowed CRN Team Wood to see and study the tiny, toxic alpha-synuclein oligomers (protein clumps) in the brain, creating a new opportunity for earlier diagnosis and better drug treatments.
Immunofluorescence source data
By onThese files include the raw, unedited, immunofluorescence images.
Western blot source data
By onSource Data for Western Blots in Main Figures 1-7 and Supplemental Figures 1, 3-5
Original data for Figures 1-7 & Figure EV1-EV4A [Hanna et al. 2024]
By onOriginal data for Figures 1-7 & Figure EV1-EV4A from Hanna et al 2024
SIFT based MATLAB script [Hanna et al 2024]
By onSIFT based MATLAB script used in the preprint Hanna et al 2024
Python code: Figure generating script [Hanna et al 2024]
By onPython code: Figure generating script used in the preprint Hanna et al 2024
ImageJ code: Analysis script_0 [Hanna et al 2024]
By onImageJ code: Analysis script_0 used in the preprint Hanna et al 2024
Script for image quantification [Wang et al 2025]
By onScript for image quantification used in Wang et al 2025
