RNA proximity sequencing reveals properties of spatial transcriptome organization in the nucleus(Dataset ID: STDS0000099)

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PMID: 31992717
PMID: 31267103
Summary
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Dataset information
Summary:
Spatial transcriptomics aims to understand how the ensemble of RNA molecules in tissues and cells is organized in 3D space. Here we introduce Proximity RNA-seq, which identifies co-localization preferences for pairs or groups of chromatin-associated, nuclear-retained and nascent RNAs in cell nuclei. Proximity RNA-seq is based on massive-throughput RNA barcoding of sub-nuclear particles in water-in-oil emulsion droplets, followed by sequencing.
Overall design:
4 Proximity RNA-Seq datasets (Pools 2, 5, 7 & 8), 2 Hi-C datasets
Technology:
Proximity RNA-seq
Platform:
GPL16791
Species:
Homo sapiens(hg38)
Tissues:
Neuron
Organ parts:
SHY neuroblasts
Submission date: 2019-04-12Update date: 2020-02-10
DOI: To be continue
Contributors
Morf J,Wingett SW,Farabella I,Cairns J,Furlan-Magaril M,Jiménez-García LF,Liu X,Craig FF,Walker S,Se
Contact: steven.wingett@babraham.ac.uk
Accessions
GEO Series Accessions: GSE129732
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] Morf J,Wingett SW,Farabella I,Cairns J,Furlan-Magaril M,Jiménez-García LF,Liu X,Craig FF,Walker S,Se. RNA proximity sequencing reveals properties of spatial transcriptome organization in the nucleus[DS/OL]. STOmicsDB, 2019[2019-04-12]. https://db.cngb.org/stomics/datasets/STDS0000099/. 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: Wingett, Steven W et al. “RNA proximity sequencing data and analysis pipeline from a human neuroblastoma nuclear transcriptome.” Scientific data vol. 7,1 35. 28 Jan. 2020, doi:10.1038/s41597-020-0372-3