• INDEPTH Academy

  • INDEPTH_Academy_Logo_E

    The INDEPTH Academy is a training resource developed by the COST Action 'Impact of Nuclear Domains On Gene Expression and Plant Traits (INDEPTH)'

    The INDEPTH Academy will deliver multimedia resources to inform how the spatial organisation of nuclear DNA is critical in the adaptation to environmental stresses.

    Many of these resources can be found on the INDEPTH Academy YouTube Channel.

    INDEPTH Academy outputs include:

    - Short webinar teaching resources that introduce functional domains of the nucleus (such as the nucleolus of nuclear envelope) and explore how chromatin dynamics influence gene expression

    - Masterclass tutorials in which technical experts will lead discussion-led sessions on experimental techniques that are important for study of the plant nucleus

    - Standardised Protocols that are linked to INDEPTH member research activities

    - Expert talks from the 2021 SEB Antwerp Main Meeting Special Session on 'Dynamic organization of the nucleus across kingdoms''.

    Upcoming events

    The INDEPTH Academy are hosting a section of the 'Dynamic organization of the nucleus across kingdoms' session in the virtual SEB Main Meeting in July 2021.


    INDEPTH Academy Masterclass Tutorials

    Celia Baroux on the 'Spatial analysis of nuclear signal distribution using Imaris and DataViz'

    Dimiter Prodanov and Sumit Vohra introduce their Active Segmentation tool for plant image analysis.

    Ruben Gutzat provides a technical webinar on Fluorescence-Activated Nuclei Sorting (FANS).

    Christophe Tatout provides a detailed description of NucleusJ 2.0 with Q+A

    Stefanie Rosa provides a detailed description of smFISH with extended Q+A

    Professor Hank Bass from Florida State University is hosting the INDEPTH Image Repository through the OMERO software.

    INDEPTH Academy Teaching Webinars

    Danny Geelen discusses the effect of temperature on sexual reproduction

    Dr Christian Chevalier introduces 'DNA-dependent fruit growth in tomato: the role of endoreduplication

    Dr Kriton Kalantidis introduces the fascinating biology of Virioids, smallest-known pathogens.

    Dr Celia Baroux introduces the background and state of the art in the knowledge about Linker Histone in plants.

    Dr Geraint Parry introduces the Plant Nuclear Pore Complex.

    Dr Monica Pradillo introducing the Role of Chromatin Domains on Plant Meiosis.

    Dr Frederic Pontvianne introduces the Function of the Plant Nucleolus.

    Francesca Lopez discusses gene dosing of ribosomal RNA and her INDEPTH STSMs

    Emilia Cepowska discusses her STSM work on Gene Loops in Stress Memory in Arabidopsis

    Gianluca Teano discusses his research on the role of Histone 1 in chromatin organisation, which has benefited from his participation in two STSMs.


    INDEPTH Academy Expert Protocols

    Hi_C-Image   Protocol for Hi-C Chromosome Confirmation Capture. This method is adapted from research in the labs of Chang Liu and Silin Zhong.

    smFISh_Image   Protocol for Single Molecular Fluorescent In Situ Hybridisation. This method is adapted from research in Stefanie Rosa's lab and provides instructions for this powerful technique for analysis of gene expression

    5_Image   Protocol for Localising Total mRNA in Plant Cells . This method is adapted by Geraint Parry for a selection of published methodologies 

    FANS_ImageProtocol for Fluorescence Activated Nuclear Sorting (FANS) for RNA extraction, DNA extraction or Chromatin Immunoprecipitation. This method is adapted from protocols developed in Ortrun Mittelsten Scheid's lab

     Protocol for Isolation of Plant Nucleolus. This method is adapted from protocols by Frederic Pontvianne

    ATAC-seq_Image Protocol for  Assay for Transposase-Accessible Chromatin (ATAC-seq ). This method is adapted from a variety of protocols from the labs of Roger Deal and Kenneth Berendzen

    MYTH_Pic Protocol for Membrane Yeast Two-Hybrid (MYTH) for analysis of targeted interactions or identification of novel interactors. This method is adapted from a variety of protocols, in particular from the lab of Christophe Tatout. 


  • Joining the INDEPTH COST Action

    If you are interested in joining Action please contact the INDEPTH Chairman stating why the research program of your lab would enhance the overall activity of the Action.

    Christophe Tatout