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| Status |
Public on May 03, 2019 |
| Title |
RNA proximity sequencing reveals properties of spatial transcriptome organization in the nucleus |
| Organism |
Homo sapiens |
| Experiment type |
Other
Expression profiling by high throughput sequencing
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| 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.
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| Overall design |
4 Proximity RNA-Seq datasets (Pools 2, 5, 7 & 8), 2 Hi-C datasets
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| Contributor(s) |
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 |
| Citation(s) |
31267103, 31992717 |
| Submission date |
Apr 12, 2019 |
| Last update date |
Feb 10, 2020 |
| Contact name |
Steven William Wingett |
| E-mail(s) |
steven.wingett@mrc-lmb.cam.ac.uk
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| Organization name |
MRC Laboratory of Molecular Biology
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| Department |
Cell Biology
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| Street address |
Francis Crick Avenue, Cambridge Biomedical Campus
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| City |
Cambridge |
| State/province |
Cambs |
| ZIP/Postal code |
CB2 0QH |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA532610 |
| SRA |
SRP192392 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE129732_Monte_Carlo_Simulation_Results.txt.gz |
13.7 Mb |
(ftp)(http) |
TXT |
| GSE129732_Pools_2_5_8_simulation_format_combined_file.txt.gz |
395.1 Mb |
(ftp)(http) |
TXT |
| GSE129732_local_RNA_connectivity.xlsx |
447.8 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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