GEO DataSets

(Submitter supplied) Thermostable reverse transcriptases are workhorse enzymes underlying nearly all modern techniques for RNA structure mapping and for transcriptome-wide discovery of RNA chemical modifications. Despite their wide use, these enzymes’ behaviors at chemical modified nucleotides remain poorly understood. Wellington-Oguri et al. recently reported an apparent loss of chemical modification within putatively unstructured polyadenosine stretches modified by dimethyl sulfate or 2’ hydroxyl acylation, as probed by reverse transcription. more...

Organism:

Human immunodeficiency virus; synthetic construct

Type:

Other

Platforms:

GPL17769 GPL28440

3 Samples

Download data: TAR

(Submitter supplied) Chemical probing has the power to provide insight into RNA conformation in vivo and in vitro, but interpreting the results depends on methods to detect the chemically modified nucleotides. Traditionally, the presence of modified bases was inferred from their ability to halt reverse transcriptase during primer extension and the locations of termination sites observed by electrophoresis or sequencing. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

20 Samples

Download data: CSV

(Submitter supplied) 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. more...

Organism:

Saccharomyces cerevisiae; Homo sapiens; Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

10 related Platforms

29 Samples

Download data: TXT

(Submitter supplied) Deciphering the conformations of RNAs in their cellular environment allows identification of RNA elements with potentially functional roles within biological contexts. Insight into the conformation of RNA in cells has been achieved using chemical probes that were developed to react specifically with flexible RNA nucleotides, or the Watson-Crick face of single-stranded nucleotides. The most widely used probes are either selective SHAPE (2'-hydroxyl acylation and primer extension) reagents that probe nucleotide flexibility, or dimethyl sulfate (DMS), which probes the base-pairing at adenine and cytosine but is unable to interrogate guanine or uracil. more...

Organism:

Homo sapiens; Mus musculus

Type:

Other

Platforms:

GPL16791 GPL17021

42 Samples

Download data: CSV

(Submitter supplied) The study aimed to characterize the mutational signatures produced by MarathonRT upon reverse transcription of modified cellular RNAs and use the signatures of validated modified rRNAs as training data for machine learning algorithms. Performance of the resulting trained algorithms was evaluated on a series of test RNAs in order to establish a general workflow for detection of RNA modifications

Organism:

Saccharomyces cerevisiae; Escherichia coli; Homo sapiens

Type:

Other

4 related Platforms

20 Samples

Download data: TXT