GEO DataSets

(Submitter supplied) The rapidly growing popularity of RNA structure probing methods is leading to increasingly large amounts of available RNA structure information. This demands the development of efficient tools for the identification of RNAs sharing regions of structural similarity by direct comparison of their reactivity profiles, hence enabling the discovery of conserved structural features. We here introduce SHAPEwarp, a largely sequence-agnostic SHAPE-guided algorithm for the identification of structurally-similar regions in RNA molecules. more...

Organism:

Severe acute respiratory syndrome-related coronavirus; Severe acute respiratory syndrome coronavirus 2

Type:

Other

Platforms:

GPL28588 GPL30986

4 Samples

Download data: WIG

(Submitter supplied) The genomes of RNA viruses encode the information required for replication in host cells both in their linear sequence and in complex higher-order structures. A subset of these RNA genome structures show clear sequence conservation, and have been extensively described for well-characterized viruses. However, the extent to which viral RNA genomes contain functional structural elements – unable to be detected by sequence alone – that nonetheless are critical to viral fitness is largely unknown. more...

Organism:

dengue virus type 1; dengue virus type 3; dengue virus type 2; dengue virus type 4

Type:

Other

4 related Platforms

12 Samples

Download data: SHAPE, TXT

(Submitter supplied) New regulatory roles continue to emerge for both natural and engineered noncoding RNAs, many of which have specific secondary and tertiary structures essential to their function. Thus there is a growing need to develop technologies that enable rapid characterization of structural features within complex RNA populations. We have developed a high-throughput technique, SHAPE-Seq, that can simultaneously measure quantitative, single nucleotide-resolution secondary and tertiary structural information for hundreds of RNA molecules of arbitrary sequence. more...

Organism:

Bacillus subtilis

Type:

Other

Platform:

GPL14181

2 Samples

Download data: SAM

(Submitter supplied) Previous reports studying similar flavivirus infections (DENV, WNV, etc.) revealed an increase in both the abundance and stability of normally short-lived cellular mRNAs. This resulted from the stalling/repression of the major 5’-3’ host exoribonuclease XRN-1 on three-helix junction structures present in the 3’-UTR of insect-borne flaviviruses. Therefore we sought to identify the endogenous mRNA abundance and stability changes induced during early and late times following Zika virus infection (PRBRAC59) in human choriocarcinoma (JAR) cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

5 Samples

Download data: BED, FASTA, TSV