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| Status |
Public on Nov 29, 2023 |
| Title |
Decoding the gene regulatory network of endosperm differentiation in maize [scRNA-seq] |
| Organism |
Zea mays |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The persistent cereal endosperm constitutes the majority of the grain volume. Dissecting the gene regulatory network underlying cereal endosperm development will facilitate yield and quality improvement of cereal crops. Here, we use single-cell transcriptomics to analyze the developing maize (Zea mays) endosperm during cell differentiation. After obtaining transcriptomic data from 17,022 single cells, we identify 12 cell clusters corresponding to five endosperm cell types and revealing complex transcriptional heterogeneity. We delineate the temporal gene expression pattern from 6 to 7 days after pollination. We profile the genomic DNA binding sites of 161 transcription factors differentially expressed between cell clusters and constructed a gene regulatory network by combining the single-cell transcriptomic data with the direct DNA-binding profiles, identifying 181 regulons containing genes encoding transcription factors along with their high-confidence targets, Furthermore, we map the regulons to endosperm cell clusters, identify cell-cluster-specific essential regulators, and experimentally validated three predicted key regulators. This study provides a framework for understanding cereal endosperm development and function at single-cell resolution.
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| Overall design |
Construction of gene regulatory networks in maize endosperm using scRNA-seq and DAP-seq
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| Citation(s) |
38167709 |
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| Submission date |
Apr 26, 2022 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Qiang Huo |
| E-mail(s) |
huoqiang@cau.edu.cn
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| Organization name |
China Agricultural University
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| Street address |
Yuanmingyuan West Road
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| City |
Beijing |
| ZIP/Postal code |
100091 |
| Country |
China |
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| Platforms (1) |
| GPL25410 |
Illumina NovaSeq 6000 (Zea mays) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE201701 |
Decoding the gene regulatory network of endosperm differentiation in maize |
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| Relations |
| BioProject |
PRJNA832419 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE201640_RAW.tar |
151.2 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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