A spatially resolved multiomic single-cell atlas of soybean development(Dataset ID: STDS0000332)

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Summary
Data
Sample
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Dataset information
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Dataset information
Summary:
Cis-regulatory elements (CREs) precisely control the spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression and chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) binding motifs controlling cell-type specification and maintenance. We identified non-cell autonomous activity of NIN-LIKE PROTEIN 7 (NLP7), the Nodule Inception (NIN) gene regulatory network and de novo enriched TF motifs in the nodule infected cells. With comprehensive developmental trajectories for endosperm and embryo, we found that 13 sucrose transporters, sharing the DOF11 binding motif, were co-up-regulated in late peripheral endosperm and identified the key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.
Overall design:
We generated a comprehensive accessible chromatin and transcriptome atlas across various cell types in soybean with scATAC-seq, snRNA-seq and spatial-RNA-seq(spRNA-seq), where we collected samples from ten major tissues at different stages of the soybean life cycle. These tissues included leaf, hypocotyl, root, nodule, young pod, and five stages of developing seeds: globular stage (GS), heart stage (HS), cotyledon stage (CS), early maturation stage (EMS), and middle maturation stage (MMS). For each tissue, we conducted scATAC-seq and snRNA-seq with at least two replicates.
Technology:
ST
Platform:
Illumina NovaSeq 6000
Species:
Glycine max
Tissues:
seeds at cotyledon stage, seeds at early maturation stage, seeds at globular stage, seeds at heart stage, hypocotyl, leaf, seeds at middle maturation stage, root with 1mm nodule, whole pod, root
Submission date: 2024-06-20Update date: 2024-08-08
DOI: To be continue
Contributors
Schmitz, Robert J.; Schmitz, Robert J; Zhang, Xuan; Luo, Ziliang; Marand, Alexandre P
Contact: contrib1
Accessions
GEO Series Accessions: GSE270392
How to cite
  • Cite database of STOmicsDB:
    [1] Xu, Zhicheng et al. "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization." Nucleic acids research vol. 52,D1 (2024): D1053-D1061. doi: 10.1093/nar/gkad933'
  • Cite visualization dataset:
    [2] Schmitz, Robert J.. A spatially resolved multiomic single-cell atlas of soybean development[DS/OL]. STOmicsDB, 2024[2024-06-20]. https://db.cngb.org/stomics/datasets/STDS0000332/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    No results.