Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

E. coli SHAPE-MaP

ABSTRACT: SHAPE-MaP probing of RNA structures in E. coli cells

PROVIDER: PRJEB23974 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2226510_1.fastq.gz	Fastqsanger.gz
	ERR2226510_2.fastq.gz	Fastqsanger.gz
	ERR2226520_1.fastq.gz	Fastqsanger.gz
	ERR2226520_2.fastq.gz	Fastqsanger.gz
	ERR2226530_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 192

Similar Datasets

Structural atlas of human primary microRNAs generated by SHAPE-MaP

Project description:MicroRNA (miRNA) maturation is critically dependent on structural features of primary transcripts (pri-miRNAs). However, the scarcity of determined pri-miRNA structures has limited our understanding of miRNA maturation. Here we employed SHAPE-MaP, a high-throughput RNA structure probing method, to unravel the secondary structures of 476 high-confidence human pri-miRNAs. Our SHAPE-based structures diverge substantially from those inferred solely from computation, particularly in the apical loop and basal segments, underlining the need for experimental data in RNA structure prediction. By comparing the structures with high-throughput processing data, we determined the optimal structural features of pri-miRNAs. The sequence determinants are influenced substantially by their structural contexts. Moreover, we identified an element termed the bulged GWG motif (bGWG) with a 3′ bulge in the lower stem, which promotes processing. Our structure-function mapping better annotates the determinants of pri-miRNA processing and offers practical implications for designing small hairpin RNAs and predicting the impacts of miRNA mutations.

2024-01-31 | GSE254361 | GEO

Complete in vivo SHAPE-MaP structure of the SARS-CoV-2 genome

Project description:SHAPE-MaP structure probing experiment was performed on SARS-CoV-2 infected Vero cells at 4 days post infection with two biological replicates. For each replciate, SHAPE-MaP includes a sample treated with 2-methylnicotinic acid imidazolide acid (modified) or a minue reagent (unmodified). NAI preferentially reacts with unpaired bases in RNA, forming acylated bases. These modifications are encoded as mutation during reverse transcripatse and library preparation. After sequencing and alignment, the reactivity profiles of 'modified' and 'unmodified' samples are used to calculate SHAPE reactivity of each base

2021-01-11 | GSE154171 | GEO

BTV Shape Map

Project description:BTV Shape Map

| PRJEB71404 | ENA

SHAPE analysis of RNA structure in living cells with unprecedented accuracy

Project description:Due to the mounting evidence that RNA structure plays a critical role in regulating almost any essential physiological as well as pathological process, being able to accurately define the folding of RNA molecules within living cells has become a crucial need. We introduce here 2-aminopyridine-3-carboxylic acid (2A3), as a general probe for the interrogation of RNA structures in vivo. 2A3 performs comparably well to NAI on naked RNA under in vitro conditions and it significantly outperforms NAI when probing RNA structure in vivo, particularly in bacteria, underlining its increased ability to permeate biological membranes. When used as a restraint to drive RNA structure prediction, data derived by SHAPE-MaP with 2A3 yields more accurate predictions than NAI-derived data. Due to its extreme efficiency and accuracy, we can anticipate that 2A3 will rapidly take over conventional SHAPE reagents for probing RNA structures both in vitro and in vivo.

2020-12-16 | GSE154563 | GEO

Optimization of SHAPE-MaP protocol

Project description:SHAPE-Map optimization

| PRJEB60419 | ENA

Enhanced DMS-MaP enables superior RNA structural analysis

Project description: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.

2023-05-12 | GSE225383 | GEO

The SHAPE-MaP experiment to identify RNA structures of pri-mir-142 variants

Project description:The SHAPE-MaP experiment to identify RNA structures of pri-mir-142 variants

| PRJNA917296 | ENA

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

RIP-PEN-SHAPE-MaP for 15.5K-interacted RNAs

Project description:RNA secondary structure is crucial for RNA mentalism, including transcription, splicing, translation, RNA-binding protein interaction as well as turnover. The kink-turn (K-turn) structure motif is is an RNA three-dimensional (3D) structure that exists in all three primary phylogenetic domains and plays vital roles in RNA metabolism. In order to investigate the K-turn secondary structure in vivo, we combined SHAPE-Map and our RIP-PEN-seq to profile the RNA structure of 15.5K-interacted RNAs.

2023-04-10 | GSE220470 | GEO

Shape of promoter antisense RNAs regulates ligand-induced transcription activation [Shape-Map]

Project description:Shape of promoter antisense RNAs regulates ligand-induced transcription activation [Shape-Map]

| PRJNA686387 | ENA