User guidance

About

RNAdt is a web-based tutorial and data portal for HTS-associated RNA structure probing methods. Users can use RNAdt to learn to implement RNA structure probing experiments with easy because the workflow of each method from its original publication is provided. For users who are interested in learning to analyze RNA structurome data, RNAdt can be used as a data portal to reach existing HTS data sets.

Of note, we may not include the complete list of RNA structure probing methods due to imperfect search and filtering strategies. We apologize to authors whose state-of-the-art methods are not included in this version of RNAdt. RNAdt promises to provide free and long-term service. In the future, RNAdt will be continuously updated and more RNA structure probing methods will be added in. RNAdt is expected to be a valuable resource to get profound insights into the RNA biology.

The source code of RNAdt has been released on GitHub. You were appreciated if you could make a contribution to this project.

Abbreviations

HTS: High-throughput sequencing.

_NA_: Not Available owing to no data from the original source, or Not Applicable.

RT: Reverse Transcription.

Definition of fields shown in the method detail page
FiledDefinition
MethodThe name of the RNA structure probing method.
YearThe year when this method was published.
NameThe full name of this method.
PublicationThe title of the article in which this method was published.
Published byThe authors of the article in which this method was published.
Publication abstractThe abstract of the article in which this method was published.
Publication dataThe HTS data alongside the article in which this method was published.
Publication doiThe DOI of the article in which this method was published.
ProbeThe probe(s) this method uses.
Probe classWhat class the probe(s) belongs to.
Probe targetWhich nucleobase or moiety the probe targets.
Target regionWhich part of the RNA strand the probe targets.
ReadoutThe method used to read structural signal (e.g. reactivity).
Scale The scale at which this method assesses RNA structure.
Structure inferredThe type of the probed high-level RNA structure.
Validated byThe RNA used to validate this method.
Validated inThe organism or biological system used to validate this method.
WorkflowThe schematic workflow of this method from its original publication.
Figure reuse licenseThe license of permission granted to RNAdt to use the original figure from its copyright holder.