Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Enhanced DMS-MaP enables superior RNA structural analysis

ABSTRACT: We develop an enhanced MaP protocol based on MarathonRT and bioinformatic optimizations which enables robust DMS probing of all four RNA nucleotides within living cells. We demonstrate this on RNA from E. coli and HEK293 cell lines.

ORGANISM(S): Escherichia coli Homo sapiens

PROVIDER: GSE225383 | GEO | 2023/05/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Enhanced DMS-MaP enables superior RNA structural analysis

Project description:Enhanced DMS-MaP enables superior RNA structural analysis

| PRJNA935379 | ENA

4U-DMS-MaP probing of nascent ribosomes

Project description:4U-DMS-MaP probing of nascent ribosomes

| PRJNA659772 | ENA

Structural characterization of ribosome variants

Project description:DMS probing of E coli ribosomes

2018-10-03 | GSE105112 | 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

PAIR-MaP visualizes RNA base pairing complexity in human and bacterial non-coding RNAs

Project description:Structure probing experiments were performed on in vitro transcripts and E. coli and human cell cultures under natively extracted (cell-free) and in-cell conditions to benchmark the performance of the newly introduced PAIR-MaP correlated chemical probing strategy for detecting RNA duplexes. Multiple-hit dimethyl sulfate (DMS) probing was done using new buffer conditions that facilitate DMS modification of all four nucleotides.

2019-08-01 | GSE135211 | GEO

Targeted DMS probing of SF3A3 5' UTR

Project description:Targeted DMS probing of SF3A3 5' UTR

| PRJNA615008 | ENA

Targeted DMS probing of SF3A3 5' UTR

Project description:To delineate the native structure of SF3A3 5'UTR, RNA was harvested from IMR90 human fibroblasts. Using specific primers and DMS-MaPSeq pipeline, we validated individual base pairing probabilities within the endogenous 5'UTR of SF3A3 (samples described as 'in vivo' transcribed). DMS-MaP-Seq is based on the principle that DMS is highly reactive to solvent-accessible, unpaired adenine (A) and cytosine (C) residues, but remains inert toward base-paired A and C engaged in Watson-Crick interactions (Rouskin et al., 2014). Using this methodology, we identify stable stem-loop structure (SL3) positioned within SF3A3 5'UTR. To further validate the functional importance of SL3, the structural point mutant (SF3A3 5'UTR mut: A55C and U95A) and rescue (SF3A3 5'UTR res: A55C and U95A and rescuing point mutations G61U and U100G) sequences of SF3A3 5'UTR were cloned into the reporter plasmid. For the validation of these mutate-and-rescue constructs, plasmids were in vitro transcribed and either used directly (samples described as 'in vitro') for DMS-MaP-Seq probing.

2021-03-25 | GSE147504 | GEO

SHAPE and DMS probing of SLNCR1 lncRNA conserved region 403-780

Project description:The goal of this study was to understand the underlying structure of nucleotides 403-780 of the lncRNA SLNCR1, in-cell and when extracted from nuclear and cytoplasmic fractions. SHAPE and DMS probing revealed that the region is largely unstructured inside and outside of the cell, and appears protein-bound in primary melanoma cells.

2019-11-07 | GSE140048 | GEO

Using DMS-MaPseq to dissect structural differences of ribosomal RNA in different SSU Processome intermediates

Project description:Ribosomes are among the largest folded RNAs, whose function depends on their structure. Nonetheless, in vitro studies indicate a propensity of rRNAs to misfold. We use a combination of DMS-MaPseq, structural analyses, biochemical experiments, and yeast genetics to dissect the final RNA folding steps of the small ribosomal subunit head.

2022-08-31 | GSE183045 | GEO

Using DMS-MaPseq to dissect structural differences of ribosomal RNA in different pre-40S intermediates

2021-06-04 | GSE160161 | GEO