‘multiOmics data analysis, integration, and visualisation protocol

• Data integration and modelling with R
• Systems biology analysis and visualization pipeline in R and Python

Data management framework

pISA-tree on GitHub

Petek, M., Zagorščak, M., Blejec, A. et al. pISA-tree - a data management framework for life science research projects using a standardised directory tree. Sci Data 9, 685 (2022). https://doi.org/10.1038/s41597-022-01805-5

Expected measurements

Factorial experiment:

• one or multiple genotypes AND/OR

• under single and multiple abiotic/biotic stressors AND/OR

• experiment duration: hours, days, ... : time-series experimental design AND/OR

• tissue: single or multiple

• Omics' strategies:

  • Hormonomics
  • Transcriptomics
  • Proteomics
  • Metabolomics
  • Phenomics
  • ...

• Combination of targeted and untargeted measurements

• Phenomics data should be preprocessed, i.e. this protocol does not include image analysis

Analysis

Protocol for the integration of multi-omics data and deep phenotyping of potato cv. Désirée under single- and combined abiotic stress responses is available at _p_ADAPTOmics

Publications

• Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato, Plant Physiology, Volume 197, Issue 4, April 2025, kiaf126, https://doi.org/10.1093/plphys/kiaf126