Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus(Dataset ID: STDS0000082)

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124
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22
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Genes: 27,515
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PMID: 32066983
Summary
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Dataset information
Summary:
We apply geographical position sequencing (Geo-seq), a method that combines laser capture microdissection (LCM) and single-cell RNA-seq technology, to investigate the heterogeneous nature of suprachiasmatic nucleus (SCN) in adult mouse. The 3D quantitative data enables spatial gene expression pattern visualization . The dataset identified genes that are coexpressed in a specific region, mark domains of similar global pattern of expression, and can be used for mapping the position of single cells dissociated from adult SCN.
Overall design:
In laser capture microdissection (LCM), hexagon grids with 40-渭m maximal radius was used and the transcriptome of each hexagon was obtained using single-cell RNA-seq technology.
Technology:
Geo-seq
Platform:
GPL21273
Species:
Mus musculus(mm10)
Tissues:
Brain
Organ parts:
Suprachiasmatic nucleus
Development stage:
8 weeks
Submission date: 2018-08-10Update date: 2020-02-21
DOI: To be continue
Contributors
Meng Zhao
Contact: shaoangwen@live.cn
Accessions
GEO Series Accessions: GSE118403
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] Meng Zhao. Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus[DS/OL]. STOmicsDB, 2018[2018-08-10]. https://db.cngb.org/stomics/datasets/STDS0000082/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    Citation: Wen, Shao'ang et al. “Spatiotemporal single-cell analysis of gene expression in the mouse suprachiasmatic nucleus.” Nature neuroscience vol. 23,3 (2020): 456-467. doi:10.1038/s41593-020-0586-x