Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications

ABSTRACT: RNA is emerging as a key regulator of a plethora of biological processes. While its study has remained elusive for decades, the recent advent of high-throughput sequencing technologies provided the unique opportunity to develop novel techniques for the study of RNA structure and post-transcriptional modifications. Nonetheless, most of the required downstream bioinformatics analyses steps are not easily reproducible, thus making the application of these techniques a prerogative of few laboratories. Here we introduce RNA Framework, an all-in-one toolkit for the analysis of most NGS-based RNA structure probing and post-transcriptional modifications mapping experiments. To prove the extreme versatility of RNA Framework, we applied it to both an in-house generated DMS-MaPseq dataset, and to a series of literature available experiments. Notably, when starting from publicly available datasets, our software easily allows replicating authors' findings. Collectively, RNA Framework provides the most complete and versatile toolkit to date for a rapid and streamlined analysis of the RNA epistructurome. RNA Framework is available for download at: http://www.rnaframework.com.

ORGANISM(S): Escherichia coli

PROVIDER: GSE111962 | GEO | 2018/06/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications

Project description:RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications

| PRJNA438686 | ENA

DMS-MaPseq: A genome-wide or targeted approach for RNA structure probing in vivo

Project description:Here we present dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase (TGIRT). DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features for each molecule, and allows genome-wide studies as well as focused investigations of low abundance RNAs. We apply DMS-MaPseq to Drosophila melanogaster ovaries—the first experimental analysis of RNA structure in an animal tissue—and demonstrate its utility in the discovery of a functional RNA structure involved in the non-canonical GUG translation initiation of the human FXR2 mRNA. Additionally, we use DMS-MaPseq to compare the in vivo structure of messages in their pre-mRNA and mature forms. These applications illustrate DMS-MaPseq’s capacity to dramatically expand our ability to monitor RNA structure in vivo.

2016-09-16 | GSE84537 | GEO

KAS-Analyzer: an integrated toolkit for exploring KAS-seq data

Project description:Kethoxal-assisted ssDNA sequencing (KAS-seq) is gaining popularity as a robust and effective approach to study the dynamics of transcriptionally engaged RNA polymerases through profiling of genome-wide single-stranded DNA (ssDNA). Its latest variant, spKAS-seq, a strand-specific version of KAS-seq, has been developed to map genome-wide R-loop structures by detecting imbalances of ssDNA on two strands. However, user-friendly, open-source, and specific bioinformatic analyzer for KAS-seq data are still lacking. Here we present KAS-Analyzer as a flexible and integrated toolkit to facilitate the analysis and interpretation of KAS-seq data. KAS-Analyzer can perform standard analyses such as quality control, read alignment, and differential RNA polymerase activity analysis. In addition, KAS-Analyzer introduces many novel features, including, but not limited to: calculation of transcriptional indexes, identification of single-stranded transcribing enhancers, and high-resolution mapping of R-loops. We use benchmark datasets to demonstrate that KAS-Analyzer provides a powerful framework to study transient transcriptional regulatory programs. KAS-Analyzer is available at https://github.com/Ruitulyu/KAS-Analyzer.

2022-07-27 | GSE202044 | GEO

Probing in vivo RNA structure with optimized DMS-MaPseq in rice

Project description:Here, we use dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to conduct a target-specific and genome-wide profile of in vivo RNA secondary structure in rice (Oryza sativa). Our study presents an optimized DMS-MaPseq for probing in vivo RNA structure in rice.

2022-04-05 | GSE197245 | GEO

A genetic toolkit for studying transposon control in the Drosophila melanogaster ovary

Project description:Argonaute proteins of the PIWI-clade, complexed with PIWI-interacting RNAs (piRNAs), protect the animal germline genome by silencing transposable elements. One of the leading experimental systems for studying piRNA biology is the Drosophila melanogaster ovary. In addition to classical mutagenesis, transgenic RNA interference (RNAi), which enables tissue-specific silencing of gene expression, plays a central role in piRNA research. Here, we establish a versatile toolkit focused on piRNA biology that integrates transgenic RNAi in the germline, GFP-marker lines for key proteins of the piRNA pathway, and reporter transgenes to establish genetic hierarchies. We compare constitutive, pan-germline RNAi with an equally potent transgenic RNAi system that is activated only upon germ cell cyst formation. Stage specific RNAi allows investigating the role of genes essential for cell survival (e.g. nuclear RNA export or the SUMOylation pathways) in piRNA-dependent and independent transposon silencing. Our work forms the basis for an expandable genetic toolkit available from the Vienna Drosophila Resource Center.

2021-05-19 | GSE174611 | GEO

The microRNA toolkit of insects

Project description:Is there a correlation between miRNA diversity and levels of organismic complexity? Exhibiting extraordinary levels of morphological and developmental complexity, insects are the most diverse animal class on earth. Their evolutionary success was in particular shaped by the innovation of holometabolan metamorphosis in endopterygotes. Previously, miRNA evolution had been linked to morphological complexity, but astonishing variation in the currently available miRNA complements of insects made this link unclear. To address this issue, we sequenced the miRNA complement of the hemimetabolan Blattella germanica and reannotated that of two other hemimetabolan species, Locusta migratoria and Acyrthosiphon pisum, and of four holometabolan species, Apis mellifera, Tribolium castaneum, Bombyx mori and Drosophila melanogaster. Our analyses show that the variation of insect miRNAs is an artefact mainly resulting from poor sampling and inaccurate miRNA annotation, and that insects share a conserved microRNA toolkit of 65 families exhibiting very low variation. For example, the evolutionary shift toward a complete metamorphosis was accompanied only by the acquisition of three and the loss of one miRNA families.

2016-11-30 | GSE83339 | GEO

Calcium Toolkit genes expression in the zebrafish brain

Project description:Zebrafish are well suited for in vivo calcium imaging because the transparency of their larvae and the ability to express calcium probes in various cell subtypes. This model organism has been used extensively to study brain development, neuronal function, and network activity. However, only a few studies have investigated calcium homeostasis and signaling in zebrafish neurons, and little is known about the proteins that are involved in these processes. Using bioinformatics analysis and available databases, the present study identified 491 genes of the zebrafish Calcium Toolkit (CaTK). Using RNA-sequencing, we then evaluated the expression of these genes in the adult zebrafish brain and found 380 hits that belonged to the CaTK. Based on quantitative real-time polymerase chain reaction arrays, we estimated the relative mRNA levels in the brain of CaTK genes at two developmental stages. In both 5 dpf larvae and adult zebrafish, the highest relative expression was observed for tmbim4, which encodes a Golgi membrane protein. The present data on CaTK genes will contribute to future applications of zebrafish as a model for in vivo and in vitro studies of Ca2+ signaling.

2019-03-05 | GSE127335 | GEO

hictk: blazing fast toolkit to work with .hic and .cool files

Project description:We developed hictk, a toolkit that can transparently operate on .hic and .cool files with excellent performance. The toolkit is written in C++ and consists of a C++ library with Python bindings as well as CLI tools to perform common operations directly from the shell, including converting between .hic and .mcool formats. We benchmark the performance of hictk and compare it with other popular tools and libraries. We conclude that hictk significantly outperforms existing tools while providing the flexibility of natively working with both file formats without code duplication.

2023-09-14 | GSE242815 | GEO

EPIC: Software Toolkit for Elution Profile-Based Inference of Protein Complexes

Project description:Heteromeric protein complexes are key macromolecular machines of the cell, but their description remains incomplete. We previously reported an experimental strategy for global characterization of native protein assemblies based on chromatographic fractionation of biological extracts coupled to precision mass spectrometry analysis (CF/MS), but the resulting data can be challenging to process and interpret. Here, we describe EPIC (Elution Profile-based Inference of Complexes), a software toolkit for automated scoring of CF/MS data for large-scale determination of high-confidence physical interaction networks and macromolecular assemblies from diverse biological specimens. As a case study, we used EPIC to map the global interactome of Caenorhabditis elegans, defining 590 putative worm protein complexes linked to diverse biological processes, including assemblies unique to nematodes. The EPIC software is freely available as a Jupyter notebook packaged in a Docker container (https://hub.docker.com/r/baderlab/bio-epic/), and the open source code is available via GitHub (https://github.com/BaderLab/EPIC).

2019-07-16 | PXD011182 | Pride

A novel antibody toolkit reveals N-terminally ubiquitinated substrates of UBE2W

Project description:Protein ubiquitination plays an essential role in cellular physiology. Contrary to canonical ubiquitination at internal lysine residues, the physiological functions of N-terminal ubiquitination remain enigmatic. To identify endogenous N-terminally-ubiquitinated substrates, we discovered four novel monoclonal antibodies that selectively recognize tryptic peptides with an N-terminal diglycine remnant, corresponding to sites of N-terminal ubiquitination. Importantly, these antibodies do not recognize isopeptide-linked diglycine (ubiquitin) modifications on lysine. We solved the structure of one such antibody bound to a Gly-Gly-Met peptide to reveal the molecular basis for its selective recognition. These antibodies were used in conjunction with mass spectrometry proteomics to map N-terminal ubiquitination sites on endogenous substrates of UBE2W. These substrates included UCHL1 and UCHL5, where N-terminal ubiquitination distinctly altered deubiquitinase (DUB) activity. This new antibody toolkit for global profiling of endogenous N-terminal ubiquitination sites will enable future work to decipher the physiological functions of N-terminal ubiquitination.

2020-11-30 | MSV000086537 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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