INDEPTH Academy

INDEPTH_Academy_Logo_E

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

In the INDEPTH Academy we will deliver multimedia resources to inform how the spatial (3D) organization of nuclear DNA is critical in the adaptation to environmental stresses.

These resources can be found on the INDEPTH Academy YouTube Channel.

Our outputs will appear over the next few months and will 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

Technical webinar on Single Molecule Fluorescence in situ Hybridization (smFISH) in Whole Mount Plant Tissues with Dr Stefanie Rosa

Wednesday January 27th 2021, 2pm GMT.

Stefanie is a leading expert using smFISH in plants and will provide a 30minute introduction to her previous work using this technique. The remainder of the webinar will provide delegates with a unique opportunity to ask Stefanie technical questions about smFISH. Unlike many webinars we welcome detailed experimental questions that someone only with Stefanie's expertise is willing and able to answer. In the lead up to the webinar we will return to registered delegates to ask if they would like to pre-submit a question.

Register for free: https://register.gotowebinar.com/register/4738573370597059087
smFISH_Webinar

Technical webinar on NucleusJ 2.0 with Professor Christophe Tatout and Dr Sophie Desset

Wednesday February 3rd 2021, 2pm GMT

Christophe, Sophie and colleagues recently published this work and they will provide a 30minute introduction to the software. The remainder of the webinar will provide delegates with a unique opportunity to ask technical questions about NucleusJ. Unlike many webinars we welcome detailed questions that someone only with Christophe and Sophie's expertise are able to answer. In the lead up to the webinar we will return to registered delegates to ask if they would like to pre-submit a question

.Register for free: https://register.gotowebinar.com/register/6773206444107335438

Tatout Webinar

INDEPTH Academy Masterclass Tutorials

Professor Hank Bass from Florida State University is hosting the INDEPTH Image Repository through the OMERO software. https://doi.org/10.24384/cqrx-5f97

INDEPTH Academy Teaching Webinars

Dr Geraint Parry introduces the Plant Nuclear Pore Complex. https://doi.org/10.24384/crg5-8x04

Dr Monica Pradillo introducing the Role of Chromatin Domains on Plant Meiosis. https://doi.org/10.24384/tnrm-mz90

Dr Frederic Pontvianne introduces the Function of the Plant Nucleolus. https://doi.org/10.24384/zn4x-0468

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

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. https://doi.org/10.24384/39fw-jm66

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 https://doi.org/10.24384/4h9v-ar37

5_Image Protocol for Localising Total mRNA in Plant Cells . This method is adapted by Geraint Parry for a selection of published methodologies https://doi.org/10.24384/m5dm-he87

FANS_Image Protocol 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 https://doi.org/10.24384/fvmf-km57

Protocol for Isolation of Plant Nucleolus. This method is adapted from protocols by Frederic Pontvianne. https://doi.org/10.24384/ycxk-1685

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

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.