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Series GSE155729 Query DataSets for GSE155729
Status Public on May 09, 2021
Title Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
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 (Ribo-STAMP) 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 Refer to individual Series
 
Citation(s) 33963355, 37784060
Submission date Aug 05, 2020
Last update date Oct 18, 2023
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 (6)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24106 MinION (Homo sapiens)
Samples (99)
GSM4709474 HEK293T-control-STAMP none
GSM4709475 HEK293T-control-STAMP low
GSM4709476 HEK293T-control-STAMP high
This SuperSeries is composed of the following SubSeries:
GSE155649 Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [RNA-seq]
GSE155708 Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]
GSE155726 Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]
Relations
BioProject PRJNA655414

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

Supplementary file Size Download File type/resource
GSE155729_RAW.tar 5.5 Gb (http)(custom) TAR (of BED, BW, TXT)
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