Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA secondary structome of different retrotransposons with DNA/protein binding

ABSTRACT: We determined the RNA secondary structure of different retrotransposon by icSHAPE. The retrotransposon has differnet states including protein bound, DNA and protein bound.

ORGANISM(S): Bombyx mori

PROVIDER: GSE226783 | GEO | 2023/05/11

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA secondary structome of different cell lines

Project description:we resolved the RNA secondary structure of human (HEK293, HeLa, K562, HepG2, H9) and mouse (mES) cells based on optimized in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). we describe a deep discriminative neural network (PrismNet) that integrates big data of RBP binding and RNA secondary structure from matched living cells and accurately models the RNA sequence and structural preferences of protein-RNA interactions in vivo, enabling precise prediction of the perturbation effects of genetic variants.

2021-02-05 | GSE145805 | GEO

RNA secondary structome of different cellular compartments in human and mouse

Project description:We resolved the RNA secondary structure of three cellular compartments including chromatin (ch), nucleoplasm(np) and cytoplasm(cy) in HEK293 and mES cells based on in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). We analyze the RNA structure dynamics among cellular compartments and different RNA processings. Also, we study which factors perturb the RNA structures.

2018-07-31 | GSE117840 | GEO

secondary structure based on icSHAPE of pre-let-7 and hDicer-TRBP bound pre-let-7

Project description:we resolved precusor let7 (pre-let-7) and human Dicer-TRBP complex bound precusor let7 (hDicer-TRBP-pre-let-7) secondary structure based on in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). We found the free pre-let-7 RNA is more flexible comparing with hDicer-TRBP-pre-7 in the double strand region [10-20nt and 50- 60 nt].

2018-02-14 | GSE110516 | GEO

secondary structure based on icSHAPE of pre-let-7 and hDicer-TRBP bound pre-let-7

Project description:secondary structure based on icSHAPE of pre-let-7 and hDicer-TRBP bound pre-let-7

| PRJNA433923 | ENA

In-cell RNA secondary structure analysis of functional SINE transcripts

Project description:SINEUPs are long non-coding RNAs which contain a functionally crucial SINE repeat element and positively regulate target mRNA translation at post-transcription level. To study secondary (2D) structure of these functional SINE-derived RNAs, various SINEUP-GFP plasmids containing different mouse SINEB2 repeat elements or human SINE FRAM repeat were transfected along with sense EGFP plasmid in HEK293T/17 cells. Total RNA in transfected cells were probed at flexible regions with NAI-N3 reagent and icSHAPE (in-vivo click selective hydroxyl acylation and profiling experiment) libraries were prepared. To further understand the structure dynamics of SINE transcripts in subcellular locations, cells were fractionated in nuclear and cytoplasmic fractions after 24 h of transfection and fraction-specific icSHAPE libraries were constructed.

2023-02-06 | GSE224534 | GEO

Regulatory impact of RNA secondary structure across the Arabidopsis thaliana transcriptome

Project description:The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, processing, and functionality. However, the global influence of this feature on plant gene expression is still for the most part unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach in conjunction with transcriptome-wide sequencing of polyA+-selected (RNA-seq), small (smRNA-seq), and ribosome-bound (ribo-seq) RNA populations to investigate the impact of RNA secondary structure on gene expression regulation in Arabidopsis. From this analysis, we find that highly unpaired and paired RNAs are strongly correlated with euchromatic and heterochromatic epigenetic histone modifications, respectively, providing further evidence that secondary structure is necessary for RNA-mediated posttranscriptional regulatory pathways. Additionally, we uncover key structural patterns across protein-coding transcripts that indicate RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in this model plant. We also reveal that RNA folding is significantly anti-correlated with overall transcript abundance, which is likely due to the increased propensity of highly structured mRNAs to be degraded and/or processed into smRNAs. Finally, we find that secondary structure affects mRNA translation, suggesting that this feature regulates plant gene expression at multiple levels. Overall, our findings provide the first global assessment of RNA folding and its significant regulatory effects in a plant transcriptome. Single-stranded RNA sequencing (ssRNA-seq) and ribosome-bound RNA sequencing (ribo-seq) in immature buds. A single replicate of each library.

2012-11-15 | E-GEOD-40209 | biostudies-arrayexpress

RNA secondary structome of different cell lines

Project description:RNA secondary structome of different cell lines

| PRJNA608297 | ENA

RNA secondary structome of SARS-CoV-2 and other 6 virus structures in the UTR regions

Project description:we resolved the RNA secondary structure of SARS-CoV-2 infected in Huh7.5.1 cells, in vitro structure of SARS-CoV-2 RNA purified from infected cells and refolded in test tube and viral RNA fragments of 7 coronaviruses including SARS-CoV-2, SARS-CoV and MERS-CoV based on in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). We built RNA structural model of SARS-CoV-2, found some functional structural elements, analysed the RNA structure conservation among different coronavirus. Also, we predicted RBP binding sites and identified some potential drug for CoVID-19 therapy.

2020-11-12 | GSE153984 | GEO

In vivo structure analysis of SINEUP RNA

Project description:To analyze SINEUP RNA secondary structure in living cells, multiple SINEUP RNA and target EGFP mRNA plasmids were transfected in HEK293T/17 cells and icSHAPE libraries were prepared.

2020-03-06 | GSE146407 | GEO

Global Analysis of the RNA-Protein Interaction and RNA Secondary Structure Landscapes Identifies Dynamic Changes During Mammalian Erythropoiesis (mRNA)

Project description:Two features of eukaryotic RNA molecules that regulate their post-transcriptional fates are RNA secondary structure and RNA-binding protein (RBP) interaction sites. However, a comprehensive global overview of the dynamic nature of these sequence features during erythropoiesis has never been obtained. Here, we use our ribonuclease-mediated structure and RBP-binding site mapping approach to reveal the global landscape of RNA secondary structure and RBP-RNA interaction sites and the dynamics of these features during this important developmental process. We identify dynamic patterns of RNA secondary structure and RBP binding that are consistently anti-correlated throughout mRNAs during erythropoiesis. Additionally, we determine a set of protein-bound sequence motifs and their dynamic structural and RBP binding contexts. Finally, using these dynamically bound sequences, we identify a number of RBPs that have known and putative key functions in post-transcriptional regulation during mammalian erythropoiesis. In total, this global analysis reveals new post-transcriptional regulators of mammalian blood cell development.

2021-07-23 | GSE148421 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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