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Series GSE155708 Query DataSets for GSE155708
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
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.
 
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.
 
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
Submission date Aug 04, 2020
Last update date May 09, 2021
Contact name Gene Yeo
E-mail(s) geneyeo@ucsd.edu
Organization name UCSD
Street address 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (2)
GPL24106 MinION (Homo sapiens)
GPL26167 PromethION (Homo sapiens)
Samples (4)
GSM4711012 control-STAMP Direct RNA
GSM4711013 control-STAMP Direct cDNA
GSM4711014 RBFOX2-STAMP Direct RNA
This SubSeries is part of SuperSeries:
GSE155729 Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes
Relations
BioProject PRJNA655251
SRA SRP275847

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE155708_RAW.tar 290.7 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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