RNA proximity sequencing reveals properties of spatial transcriptome organization in the nucleus
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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 datasetsTechnology:
Proximity RNA-seq
Platform:
GPL16791
Species:
Homo sapiens(hg38)
Tissues:
Neuron
Organ parts:
SHY neuroblasts
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/s41597-020-0372-3Submission date: 2019-04-12Update date: 2020-02-10
Contributors
Morf J; Wingett SW; Farabella I; Cairns J; Furlan-Magaril M; Jiménez-García LF; Liu X; Craig FF; Walker S; Segonds-Pichon A; Andrews S; Marti-Renom MA; Fraser P
Contact: steven.wingett@babraham.ac.uk
Accessions
GEO Series Accessions:
GSE129732