Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development

Dataset description

This Zenodo dataset contains processed and intermediate spatial transcriptomic data from serial cross-sections of maize seedling shoot apices. The dataset comprises 14 biological replicates (seedlings) generated using 10x Genomics Visium Spatial Gene Expression slides. Raw Visium sequencing reads are deposited in NCBI BioProjects PRJNA805024 and PRJNA804974. 
Processed spatial transcriptomics data is GEO GSE196882.

Individual RDS files are provided for the following samples: UL01, UL02, UL04, VR01, VR02, VR03, VR04, DQ01, DQ02, DQ03, DQ04, DQ06, DQ07, and DQ08. Each file contains the processed spatial transcriptomic object for one biological replicate, including gene-expression data, spatial coordinates, quality-control information, and available sample, section, and anatomical-domain metadata. .loom files are for scVelo analysis.

Three combined RDS objects are also included:

• sc_merged_filter_SCT2_inte.rds: the combined scRNA dataset used for normalization, integration, clustering (SRA SRR11943512 and SRR11943513).

• maize_shoot_14samples_SCT_harmony_seurat_v5.rds  : the subset used for analyses focusing on the shoot apical meristem and developing embryonic leaf domains (SAM, P1_P2, P3, P4, P5, coleoptile, co_v).

• XGE202122_S5_subset_embleaf_harmony_join.rds  : the subset used for analyses focusing on the developing embryonic leaf domains (SAM, P1_P2, P3, P4, P5).

The corresponding Space Ranger output is provided for each sample. These files include the feature–barcode matrices, spatial coordinates, tissue images, scale factors, pipeline metadata, Loupe Browser .cloupe files, and web_summary.html reports. The .cloupe files enable interactive examination of gene expression and tissue-covered spots in Loupe Browser, whereas the web summaries provide sequencing, mapping, tissue-detection, and gene-detection quality-control metrics.

These data support reproduction of the quality-control, section-splitting, SCTransform normalization, Harmony integration, clustering, anatomical-domain annotation, pseudobulk, developmental-expression, and three-dimensional reconstruction workflows described in the accompanying Bio-protocol article (Title: Serial Cryosectioning for the Spatial Transcriptomics of Maize Embryonic Leaves). Codes are deposited in the Github (https://github.com/bomacchih/maize_shoot_data_process_v2).

The original application of this dataset was reported in Wu et al. (2026), “Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development,” Plant Biotechnology Journal. https://doi.org/10.1111/pbi.70515