Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns(Dataset ID: STDS0000079)

0
|
639
|
1,083
|
Genes: 17,877
|
PMID: 30416013
Summary
Visualization
Data
Analysis results
Related
Sample
Catalog
Dataset information
Contributors
Accessions
How to cite
Dataset information
Summary:
To advance our understanding of the genetic programs that drive cell and tissue specialization, it is necessary to obtain a comprehensive overview of gene expression patterns. Here, we have used spatial | transcriptomics to generate high-resolution, anteroposterior gene expression maps of C. elegans males and hermaphrodites. To explore these maps, we have developed computational methods for discovering region- and tissue-specific genes. | We have found extensive sex-specific gene expression differences in the germline and sperm and discovered genes that are specifically expressed in the male reproductive tract. These include a group of uncharacterized genes that encode small secreted proteins that are required for male fertility. We conclude that spatial gene expression maps provide a powerful resource for identifying tissue-specific gene functions in C. elegans. Importantly, we found that expression maps from different animals can be precisely aligned, enabling transcriptome-wide comparisons of gene expression patterns.
Overall design:
Spatial transcriptomics by RNA-tomography (TomoSeq) on 20um sections
Technology:
Tomo-seq
Platform:
GPL13657
Species:
Caenorhabditis elegans(WS249)
Submission date: 2018-05-21Update date: 2018-11-05
DOI: To be continue
Contributors
Annabel Ebbing,Abel Vertesy,Marco Betist,Bastiaan Spanjaard,Jan P Junker,Eugene Berezikov,Alexander
Accessions
GEO Series Accessions: GSE114723
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] Annabel Ebbing,Abel Vertesy,Marco Betist,Bastiaan Spanjaard,Jan P Junker,Eugene Berezikov,Alexander . Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns[DS/OL]. STOmicsDB, 2018[2018-05-21]. https://db.cngb.org/stomics/datasets/STDS0000079/. 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: Ebbing, Annabel et al. “Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns.” Developmental cell vol. 47,6 (2018): 801-813.e6. doi:10.1016/j.devcel.2018.10.016