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Status |
Public on May 09, 2021 |
Title |
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP] |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
RNA binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet, the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC Mediated Profiling), which efficiently detects RBP RNA interactions. STAMP does not rely on UV crosslinking or immunoprecipitation and, when coupled with single cell capture, can identify RBP and cell type specific RNA protein interactions for multiple RBPs and cell types in single pooled experiments. Pairing STAMP with long read sequencing also yields RBP target sites for full length isoforms. Finally, conducting STAMP using small ribosomal subunits (RiboSTAMP) allows analysis of transcriptome wide ribosome association in single cells. STAMP enables the study of RBP RNA interactomes and translational landscapes with unprecedented cellular resolution.
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Overall design |
This data was generated using a strategy for immunoprecipitation-free detection of protein-RNA interactions by fusion of RNA binding proteins and ribosomal subunits to the C-to-U RNA editing enzyme APOBEC1 and quantification of interaction-driven edits by sequencing, to allow interaction detection on long-read and single-cell platforms.
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Contributor(s) |
Brannan K, Yee B, Chaim IA, Lorenz D, Marina R, Madrigal AA, Dong K, Kofman E, Jagannatha P, Yeo GW |
Citation(s) |
33963355 |
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Submission date |
Aug 04, 2020 |
Last update date |
May 09, 2021 |
Contact name |
Gene Yeo |
E-mail(s) |
geneyeo@ucsd.edu
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Organization name |
UCSD
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Street address |
2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
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City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92037 |
Country |
USA |
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Platforms (2) |
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Samples (4)
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This SubSeries is part of SuperSeries: |
GSE155729 |
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes |
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Relations |
BioProject |
PRJNA655251 |
SRA |
SRP275847 |