Spatial and single-cell expression analyses reveal complex expression domains in early wheat spike development

https://doi.org/10.5281/zenodo.15748837
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posted on 2025-08-20, 02:54 authored by xiaosa Xu, Huiqiong Lin, Junli Zhang, German Burguener, Francine Paraiso, Kun Li, Connor Tumelty, Chengxia Li, Yuchen Liu, Jorge Dubcovsky

These are the scripts and files used in the wheat spatial transcriptomic and single-cell sequencing study. This update added scripts and data for smFISH gene imputation, cellular trajectories using Monocle 3, and gene network analysis. We also added the source file for the visualization website for displaying smFISH original and imputed genes. We also corrected the smFISH stage W3.25 to W3.5.

Funding

Howard Hughes Medical Institute

National Institute of Food and Agriculture: 2022-68013-3643

National Institute of Food and Agriculture: 2022-67013-36209

National Institute of Food and Agriculture: CA-D-PLB-2850-H

University of California, Davis

History

Related Materials

1.
DOI - Is supplement to 10.1101/2025.02.15.638402

Publisher

Zenodo

Theme

Not specified

ISO Topic Category

biota
farming

National Agricultural Library Thesaurus terms

transcriptomics; genes; Internet; wheat

Pending citation

Public Access Level

Public

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Keywords

wheat spatial transcriptomics spike development single-molecule fluorescence in situ hybridization single-cell RNA sequencing co-expression analysis gene expression Transcription Factors

Licence

CC BY 4.0