Published November 18, 2021 | Version v1
Software Open

AP-4-mediated axonal transport controls endocannabinoid production in neurons - Image analysis pipelines

Creators

  • 1. Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
  • 2. Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
  • 3. Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Functional Neuroanatomy, Institute of Anatomy and Cell Biology, Heidelberg University, INF 307, Heidelberg 69120, Germany
  • 4. Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Department of Pharmacy and PhD Program in Drug Discovery and Development, University of Salerno, 132-84084 Fisciano, Salerno, Italy
  • 5. Department of Neurology, The F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA

Contributors

  • 1. Max Planck Institute of Biochemistry, Martinsried 82152, Germany

Description

Image analysis pipelines from the article "AP-4-mediated axonal transport controls endocannabinoid production in neurons", published in Nature Communications by Davies et al.

DAGLB_vs_TGN46_analysis_HeLa_cells_v3.1.9.cppipe - Cell Profiler (version 3.1.9) script used to analyse data shown in Fig. 2a, b and S2a, b.

DAGLB_vs_TGN46_analysis_patient_neurons_v3.1.9.cppipe - Cell Profiler (version 3.1.9) script used to analyse data shown in Fig. 6a, b.

DAGLB_vs_TGN46_analysis_SH-SY5Y_neuronal_cells_v3.1.9.cppipe - Cell Profiler (version 3.1.9) script used to analyse data shown in Fig. 2c, d and S2c, d.

spot_colocalization_analysis.ijm - ImageJ (version 2.1.0) script used to analyse data shown in Fig. 5 and S4.

High-throughput confocal imaging_MetaXpress_settings.docx - settings used for MetaXpress (version 6.7.0.211) to analyse data shown in Fig. 6c, e, f and S5b.

Neurite outgrowth assays_IncuCyte_settings.docx - settings used for the Incucyte® Neurotrack Analysis Software Module in IncuCyte Controller (version 2020B)  to analyse data shown in Fig. 7e-h, S6b-d and S7a-f.

See article for methods and further detail.

Notes

This work was funded by the German Research Foundation (DFG/Gottfried Wilhelm Leibniz Prize MA 1764/2-1) and the Max Planck Society for the Advancement of Science. A.K.D. received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 896725 and a Humboldt Research Fellowship. D.E.-F. had support from the CureAP4 Foundation, the Spastic Paraplegia Foundation, the National Institute of Health / National Institute of Neurological Disorders and Stroke (2R25NS070682 & 1K08NS123552-01) and the National Institutes of Health (BCH IDDRC, 1U54HD090255). M.Z. received scholarships from the DAAD (German National Exchange Service) and the German National Academic Foundation. J.E.A. is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) 270949263/GRK2162, the DAAD (German National Exchange Service), the German National Academic Foundation and the Max Weber-Program of the State of Bavaria.

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Additional details

Related works

Is supplement to
Dataset: 10.5281/zenodo.5696988 (DOI)
Dataset: 10.5281/zenodo.5698395 (DOI)
Dataset: 10.5281/zenodo.5644233 (DOI)

Funding

RARE MAPS – Dynamic proteomic maps of stem cell-derived neurons as a mechanistic discovery pipeline for rare neurological disease 896725
European Commission
CH/BIDMC/Harvard Medical School Neurology Resident Research Education Program Competing Renewal 2R25NS070682-06
National Institutes of Health