Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]

ABSTRACT: Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]

PROVIDER: PRJNA700773 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13663731_subreads.fastq.gz	Fastqsanger.gz
	SRR13663732_subreads.fastq.gz	Fastqsanger.gz
	SRR13663733_subreads.fastq.gz	Fastqsanger.gz
	SRR13663734_subreads.fastq.gz	Fastqsanger.gz
	SRR13663735_subreads.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 30

Similar Datasets

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes

Project description:Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes

| PRJNA655414 | ENA

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]

Project description:Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]

| PRJNA655419 | ENA

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]

Project description:Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]

| PRJNA655251 | ENA

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_new_eclip]

Project description:Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_new_eclip]

| PRJNA700720 | ENA

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [RNA-seq]

Project description:Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [RNA-seq]

| PRJNA655121 | ENA

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]

Project description:Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]

| PRJNA655413 | ENA

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.

Project description: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 ultraviolet cross-linking or immunoprecipitation and, when coupled with single-cell capture, can identify RBP-specific and cell-type-specific RNA-protein interactions for multiple RBPs and cell types in single, pooled experiments. Pairing STAMP with long-read sequencing yields RBP target sites in an isoform-specific manner. Finally, Ribo-STAMP leverages small ribosomal subunits to measure transcriptome-wide ribosome association in single cells. STAMP enables the study of RBP-RNA interactomes and translational landscapes with unprecedented cellular resolution.

| S-EPMC8148648 | biostudies-literature

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes

Project description: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.

2021-05-09 | GSE155729 | GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_new_eclip]

Project description: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.

2021-05-09 | GSE166402 | GEO

Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]

Project description: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.

2021-05-09 | GSE155728 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data