Q&A Feb 25, 2026

BrU-labeling and immunoprecipitation of newly synthesized RNA Anne Kruse Hollensen1, Christian Kroun Damgaard11Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark ProtocolSeeding of cellsSeed cells in eight p6 dishes per series of samples6 ml cell culture medium/dish PulseAspirate 4 ml of medium from each plate and pool medium from each series of samples. For each series of samples:For one dish (–BrU): Aspirate the remaining medium from the cells and add 3 ml of the ...

Q&A Feb 24, 2026

Hierarchical Cell Type Annotation Based on scANVIOverviewTo provide a standardized method for annotating cell types at different resolutions, this protocol describes a hierarchical cell type annotation workflow based on scANVI. The method enables multi-resolution annotation of single-cell RNA-seq datasets by:First identifying broad cell classes (primary cell types).Then refining annotations to more specific cell types within each class.Optionally extending to additional hierarchical levels.Integ...

Q&A Feb 24, 2026

Electroconvulsive Stimulation (ECS) ProcedureEri Segi-Nishida1, Katsunori Kobayashi21Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo, Japan.2Department of System Neurophysiology, Wakayama Medical University, Wakayama, Japan. AbstractElectroconvulsive therapy (ECT) is an effective treatment for medication-resistant depression. Although ECT has been used for many decades, its cellular mechanism of action is not fully understood. ...

Q&A Feb 18, 2026

Group-based Minimum Spanning Tree Correlation NetworkAuthors: Camilo Espinosa Bernal, Nima Aghaeepour The R script outlined below and attached as a supplementary txt file represent a user-friendly template to generate a group-based MST of a correlation network of clinical features for which predictive multiomic models have been built. # "# Generic Multi-Omic MST (Minimum Spanning Tree) Template# ========================================================# INPUTS REQUIRED# ---------------# 1. cl...

Q&A Feb 10, 2026

Anti-acetylated tubulin IF – Nerve IFKaylee Wells April 2020  Day 1 Primary Antibody Solution:Anti-acetylated tubulin, T7451 mouse monoclonal (Located in small -20 ℃)1:1500 dilution in 0.5% BSA (BSA made in PBST) PBS x2 (10 min)Pap pen around the sections and let dry ( >1 hour)PBS (10 min)0.5% Trition X in PBST (5 min)Block in 0.5% BSA in PBST (>2 hours)Incubate with primary antibody (overnight) at 4 ℃ in humidification chamber Day 2 Secondary Antibody Solution:Goat-anti-mouse 488A11001 – ...

Q&A Feb 5, 2026

Preparation of acute brain slicesComplete growth media composition (with 5% serum and NGF+/GDNF+):Prepare 100ml slice culture with 5% serum Mix 40 ml MEM (Minimal essential medium, INV-42360032, Invitrogen), 20 ml BME (Basal medium eagle, INV-21010046, Invitrogen), 5 ml of 5% heat inactivated horse serum (INV-26050070, Invitrogen), 0.8 ml Glutamax (Thermo Fischer Scientific, Cat# 35050061), 0.8 ml Penstrep (Thermo Fischer Scientific, Cat# 15140122), 1.1 ml Glucose (45% w/v, Sigma-Aldrich, Cat# A...

Q&A Feb 5, 2026

Determination of BV2 Microglial Phagocytic Activity (Fluorescent Microspheres / FluoSpheres Assay; Flow Cytometry/Microscopy) OverviewThis assay quantifies phagocytosis of fluorescent carboxylate-modified microspheres by BV2 microglia. After exposure to the test compound, cells are incubated with FluoSpheres, washed to remove non-internalized beads, detached with Accutase containing Hoechst 33342 to identify nuclei, and analyzed by flow cytometry. Phagocytosis is reported as the percentage of Fl...

Q&A Jan 31, 2026

Lentiviral Packaging, Concentration, and Transduction  Introduction: This protocol describes the production, concentration, and usage of second generation VSV-G pseudo typed lentiviruses for gene delivery in mammalian tissue culture. Growing Packaging Cells: Grow 293T viral packaging cells in DMEM containing 4.5 g/L glucose and 110 mg/mL sodium pyruvate, supplemented with 10% FCS, 1% L-glutamine, and 1% penicillin/streptomycin. Passage 90% confluent cultures by trypsinization and re-seed 1:5 or ...

Q&A Jan 28, 2026

Immunofluorescence ProtocolQuintana lab Rinse sections of antifreeze solution with PBS pH 7.4........................…………………………................. 3x5’Block sections with PBS 0.2% Triton X-100 + 10% normal donkey serum (NDS) (9ml +1ml) ......…....... 1h at RTIncubate with primary antibody in PBS + 0.2% Triton X-100 + 1% NDS (9.9ml +0.1ml)...........…............ ON at 4ºCWash with PBS 0.2 Triton X-100.....................…………………………………………………….................. 3x5’Incubate with secondary antibody P...

Q&A Jan 26, 2026

Co-immunoprecipitation (co-IP) Following SUMOylation/Ubiquitination Perturbation(TAK-981/TAK-243 treatment with NEM-preserved, non-denaturing lysis)OverviewThis protocol describes the workflow for treating cells with TAK-243 (ubiquitin E1/UBA1 inhibitor) and/or TAK-981 (SUMO E1 inhibitor), harvesting cells under cold conditions, preparing NEM-preserved non-denaturing lysates, and performing co-immunoprecipitation (co-IP) for downstream immunoblot analysis. Because SUMO conjugates can be lost dur...