Published September 28, 2025 | Version Version 1.0.1 — Minor corrections in column labels. Metadata in v1.0.0 was insufficient; this version provides corrected labels. No new data were added.
Dataset Restricted

Thesis - Supplementary data 3.2. TPMs for all IWGSC RefSeq v1.1 genes in sub-spike RNA-seq samples

Authors/Creators

  • 1. ROR icon John Innes Centre
  • 2. ROR icon University of East Anglia

Description

Description:
This dataset contains RNA-seq derived transcript per million (TPM) values for all wheat genes expressed in the sub-spike tissue. It also includes differential expression results generated using DESeq2, and multiple functional annotations integrated from external sources to aid interpretation.

Content overview:

  • TPM expression matrices

  • Differential expression (DE) results (DESeq2 outputs)

  • Candidate gene lists

  • Functional annotations including:

    • Homoeologue group numbers and TF family assignments from Evans et al., 2022 (doi: 10.1093/g3journal/jkac147)

    • Hormone-related annotations from Max et al., 2022 (Zenodo dataset, doi: 10.5281/zenodo.7082848)

    • Homoeologue group numbers and InterPro annotations from Ensembl Plants

    • Gene Ontology (GO) term: IWGSC RefSeq v2.1

    • Functional descriptions from FunRiceGenes

    • Comparative analysis to RNA-seq in barley: Walla et al., 2020 (doi: 10.1104/pp.20.00087)

Files

Restricted

The record is publicly accessible, but files are restricted. <a href="https://zenodo.org/account/settings/login?next=https://zenodo.org/records/17220087">Log in</a> to check if you have access.

Additional details

Is supplemented by
Dataset: 10.1093/g3journal/jkac147 (DOI)
Dataset: 10.5281/zenodo.7082848 (DOI)
Other: http://plants.ensembl.org (URL)
Other: https://funricegenes.github.io/ (URL)
References
Dataset: 10.1104/pp.20.00087 (DOI)
Publication: 10.1126/science.aar7191 (DOI)

References

  • Evans, C.E., Arunkumar, R. and Borrill, P., 2022. Transcription factor retention through multiple polyploidization steps in wheat. G3, 12(8), p.jkac147.
  • Walla, A., Wilma van Esse, G., Kirschner, G.K., Guo, G., Brünje, A., Finkemeier, I., Simon, R. and von Korff, M., 2020. An acyl-CoA N-acyltransferase regulates meristem phase change and plant architecture in barley. Plant Physiology, 183(3), pp.1088-1109.
  • Jones, M.R.W., Long, K., Phillips, A. & Uauy, C. (2022) Collation and orthology-based identification of hormone-related genes in bread wheat [Dataset]. Zenodo. doi:10.5281/zenodo.7082848
  • Ensembl plants: http://plants.ensembl.org/index.html
  • Funricegenes: https://funricegenes.github.io/
  • Hernández Molina, P., Appels, R., Eversole, K., Stein, N. and International Wheat Genome Sequencing Consortium, 2018, August. Shifting the limits in wheat research and breeding using a fully annotated reference genome. American Association for the Advancement of Science.