RNA structure in K562 cells

Reveal RNA structure and protein interactions

Secondary structure is a critical regulator of RNA biology, and the folding of an RNA depends on both its sequence and cellular factors such as RNA-binding proteins. Since in silico predictions cannot account for these factors, predictions are often inaccurate.

eSHAPE uses chemical probing to directly determine RNA structure in the cellular context. In this deeply sequencing dataset we have performed transcriptome-wide profiling of UTR usage and RNA structure, providing an unparalleled view of UTR and coding sequence structure for developing therapeutics and AI models.

Technology:

eSHAPE, End-Seq

Sample:

K562 cell line

Use:

Drug development and AI model training

Complete data, comprehensive analyses

This dataset includes aligned sequencing data to support your own discoveries as well as analysis performed by our internal bioinformatics team to reveal key insights into RNA structure.

Explore the data with interactive reports

To get to actionable insights faster we have generated interactive reports for every covered gene in the transcriptome. These reports include tables and interactive plots for data exploration.

Example of our eSHAPE report which provides interactive plots and searchable tables.

Determine RNA structure

eSHAPE reactivity is a measure of how much a nucleotide is able to react with the chemical probe we use to determine RNA structure, where increased reactivity indicates an increased probability that the nucleotide is unpaired. This reactivity can be used as an input to RNA folding algorithms to guide the folding to a more accurate final structure.

eSHAPE-supported structure of a gene in the context of cellular factors such as RNA-binding proteins.

Find protein binding

In this dataset we have performed both in vitro (without cellular factors) and in cellulo (with cellular factors) eSHAPE. By comparing the reactivity of nucleotides in cells versus the in vitro reactivity, we can detect bases that directly interact with RNA-binding proteins (RBPs).

eSHAPE-based identification of protein binding sites on the gene FTL that are known to be bound by the RBP IRP1.

Are you interested in performing an eSHAPE experiment in your specific system? Contact us today to start a project with our team of RNA experts.

Contact us today to start a project with our team of RNA experts.

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