Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ERNA: A graphic user interface-based tool for RNA sequencing data analysis [mRNA-Seq]

ABSTRACT: we performed RNA sequencing analysis using 10 tissue samples from human prostate and evaluated efficiency and accuracy of eRNA on mRNA-seq data analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE53450 | GEO | 2014/06/01

SECONDARY ACCESSION(S): PRJNA232040

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

eRNA: A graphic user interface-based tool for RNA sequencing data analysis [mRNA-Seq]

Project description:we performed RNA sequencing analysis using 10 tissue samples from human prostate and evaluated efficiency and accuracy of eRNA on mRNA-seq data analysis. We sequenced mRNAs from the 10 human tissue samples. After that, we identified mRNAs in these samples against known human genes.

2014-06-01 | E-GEOD-53450 | biostudies-arrayexpress

eRNA: A graphic user interface-based tool for RNA sequencing data analysis [microRNA-Seq]

Project description:we performed RNA sequencing analysis using 7 human plasma samples and evaluated efficiency and accuracy of eRNA on miRNA-seq data analysis.

2014-06-01 | GSE53451 | GEO

eRNA: A graphic user interface-based tool for RNA sequencing data analysis [microRNA-Seq]

Project description:we performed RNA sequencing analysis using 7 human plasma samples and evaluated efficiency and accuracy of eRNA on miRNA-seq data analysis. We sequenced microRNAs from the 7 human tissue samples with replicates (A1/A8, B2/B9, C3/C10, D4/D11, E5/E12, F6/F13, G7/G14) using NEBNext Multiplex Small RNA library Prep Set from New England Biolab (NEB). After that, we identified miRNAs in these plasma samples against known human matured miRNAs.

2014-06-01 | E-GEOD-53451 | biostudies-arrayexpress

eRNA: A graphic user interface-based tool for RNA sequencing data analysis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-06-01 | E-GEOD-53452 | biostudies-arrayexpress

eRNA: A graphic user interface-based tool for RNA sequencing data analysis

Project description:This SuperSeries is composed of the SubSeries listed below.

2014-06-01 | GSE53452 | GEO

eRNA: a graphic user interface-based tool optimized for large data analysis from high-throughput RNA sequencing.

Project description: Not available

| S-EPMC4029068 | biostudies-literature

GenePiper, a Graphical User Interface Tool for Microbiome Sequence Data Mining.

Project description: Not available

| S-EPMC6940285 | biostudies-literature

iMet: A graphical user interface software tool to merge metabolic networks.

Project description: Not available

| S-EPMC6587100 | biostudies-literature

A comparison of natural user interface and graphical user interface for narrative in HMD-based augmented reality.

Project description: Not available

| S-EPMC8717307 | biostudies-literature

Systematic Functional Characterization of Antisense eRNA of Protocadherin alpha HS5-1 Enhancer

Project description:Enhancers generate bidirectional noncoding enhancer RNAs (eRNA) that may regulate gene expression. At present, the eRNA function remains enigmatic. Here, we report a 5’ capped antisense eRNA PEARL (Pcdh eRNA associated with R-loop formation) that is transcribed from the protocadherin (Pcdh) alpha HS5-1 enhancer region. Through loss- and gain-of-function experiments with CRISPR/Cas9 DNA-fragment editing, CRISPRi, and CRISPRa as well as locked nucleic acid strategies, in conjunction with ChIRP, MeDIP, DRIP, QHR-4C, and HiChIP experiments, we find that PEARL regulates Pcdh alpha gene expression by forming local RNA-DNA duplexes (R-loops) in situ within the HS5-1 enhancer region to promote long-distance chromatin interactions between distal enhancer and target promoter. In particular, increased levels of eRNA PEARL via perturbing transcription elongation factor SPT6 leads to strengthened local three-dimensional chromatin organization within the Pcdh superTAD. These findings have important implications regarding molecular mechanisms by which the HS5-1 enhancer regulates stochastic Pcdh alpha promoter choice in single cells in the brain.

2021-10-02 | GSE148958 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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