MaizeOmics
MaizeOmics
This single-cell RNA sequencing dataset contains 17,022 high-quality cells from maize (B73 inbred line) endosperm tissue collected at 6-7 days after pollination (DAP). The dataset captures the cellular heterogeneity and gene regulatory networks during early endosperm differentiation, including multiple cell types such as aleurone (AL), starchy endosperm (SE), basal endosperm transfer layer (BETL), embryo surrounding region (ESR), and endosperm adjacent to scutellum (EAS). Expression of 25,365 genes was detected across all cells. The metadata includes basic cell information (cluster identity, cell type annotation, QC metrics), cell cycle phase assignments, and activity scores for 161 transcription factor regulons and 10 regulon modules. These regulons were constructed by integrating scRNA-seq data with ampDAP-seq-derived transcription factor binding sites, providing insights into the gene regulatory networks governing endosperm cell fate specification and differentiation.
| Field Name | Description |
|---|---|
| ClusterID | Cell cluster identification number from unsupervised clustering analysis |
| Cell Type | Annotated endosperm cell type (AL, SE, BETL, ESR, EAS, etc.) |
| orig.ident | Original sample identity indicating biological replicate |
| nCount_RNA | Total UMI counts per cell |
| nFeature_RNA | Number of genes detected per cell |
| percent.mt | Percentage of mitochondrial gene expression |
| log10GenesPerUMI | Log10 of genes per UMI, indicating cell complexity |
| seurat_clusters | Cluster number from Seurat analysis |
| Day | Days after pollination (DAP) when sample was collected |
| S.Score | S phase cell cycle score |
| G2M.Score | G2/M phase cell cycle score |
| Phase | Cell cycle phase (G1, S, or G2M) |
| THX35 to UB3 | Regulon activity scores (RAS) for 161 transcription factors, representing the activity of TF-target gene regulatory units derived from integrated scRNA-seq and ampDAP-seq data |
| M1-M10 | Activity scores for 10 regulon modules representing coordinated transcription factor networks that regulate endosperm cell type development |
Yuan, Y#., Huo, Q#., Zhang, Z., Wang, Q., Wang, J., Chang, S., Cai, P., Song, K. M., Galbraith, D. W., Zhang, W., Huang, L., Song, R*. & Ma, Z*. Decoding the gene regulatory network of endosperm differentiation in maize. Nat. Commun. 15, 34 (2024).