Course content

These materials were part of the live ‘Plant genomes: From data to discovery’. Please refer to the course page and programme of the last edition of this course, in November 2024, to check details about this live event and the original programme.

The content table below outlines the different sessions that were included in the course, as well as the format of the materials (slides/videos/practicals) and each session’s trainer. Either proceed through the materials using the arrows at the end of each page or pick your topic of interest from the table below to skip straight to it.

 Presentation slides –  View or download the slides

 Recorded lectures – Watch the lecture videos 

 Practicals – View or download the slides, exercises, datasets, analysis scripts and results

Format	Subject	Trainer
	From sequence submission and gene retrieval to variant annotation
	An introduction to Ensembl Plants	Louisse Paola Mirabueno
	From sequence submission and gene retrieval to variant annotation with Ensembl	Louisse Paola Mirabueno
	From sequence submission and gene retrieval to variant annotation with European Nucleotide Archive	Maira Ihsan
	From sequence submission and gene retrieval to variant annotation with European Variation Archive	Dona Shaju and Timothe Cezard
	Gene expression and conservation
	Exploring gene function, expression and conservation with Gramene	Andrew Olson and Marcela Tello-Ruiz
	Exploring functional conservation and expression of a gene family with Ensembl	Louisse Paola Mirabueno
	Exploring gene expression with Expression Atlas	Silvie Fexova and Pedro Madrigal
	From differentially expressed genes at bulk level to the Single Cell Gene Expression Atlas resource	Silvie Fexova and Pedro Madrigal
	From differentially expressed genes to functional characterisation
	From differentially expressed genes to functional characterisation of proteins and metabolome data with MetaboLights	Noemi Tejera
	From differentially expressed genes to functional characterisation of proteins with PRIDE	Deepti Kundu
	Field based experiments and phenotyping
	Everything, everywhere, all at once: tools and databases for managing field based experiments with Germinate	Paul Shaw and Sebastian Raubach
	GridScore NEXT – One tool to solve all your manual phenotyping needs	Sebastian Raubach and Paul Shaw
	BioImage Archive: seeing is believing	Matthew Hartley and Aybuke Yoldas
	Keynote lectures
	Tree of Life genome assembly: challenges and opportunities for plant genomes	Shane McCarthy
	Studying plant and soil microbiomes using MGnify	Robert Finn
	Contextualising your results with AlphaFoldDB and 3D-Beacons	Jennifer Fleming