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miRTRAP specifications

Information


Unique identifier OMICS_14628
Name miRTRAP
Alternative name miRNA Tests for Read Analysis and Prediction
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

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Publication for miRNA Tests for Read Analysis and Prediction

miRTRAP in publications

 (12)
PMCID: 5849194
PMID: 29560130
DOI: 10.18632/oncotarget.24495

[…] identical fashion using a mir-20 antagomir or a non-targeting control (exiqon)., verification of as cxcl8 mrna as the target of endogenous mir-20a was performed by rna immunoprecipitation using the mirtrap system following the manufacturer's instructions (takara). human colon fibroblasts plated in 10 cm dishes (90% confluency) were co-transfected with 500 pmoles of the mir-20a-5p duplex […]

PMCID: 5808213
PMID: 29467792
DOI: 10.3389/fgene.2018.00022

[…] there are several tools for mirna-seq data analysis and some have been evaluated for different purposes in previous studies. compared eight tools: mirdeep (), miranalyzer (), mirexpress (), mirtrap (), dsap (), mirtools (), mirena (), mirnakey (), and mireap (). they selected three data sets (caenorhabditis elegans, gallus gallus, and human embryonic stem cells) to evaluate […]

PMCID: 5716067
PMID: 29036674
DOI: 10.1093/nar/gkx834

[…] hairpin could also be visualized to verify the mirna* sequence., we systematically compared mirvial with six existing mirna prediction methods. three of them focus on animal species – mirdeep2 (), mirtrap () and mirena () – and the other three are tailored to plans – mirdeep-p (), mirplant () and mira (). if the six tools have parameters similar to the ones in mirvial, we used the same values […]

PMCID: 5399378
PMID: 28427349
DOI: 10.1186/s12864-017-3707-5

[…] to 285 families, were previously identified and deposited in mirbase. these mirnas were predicted from mirna-seq data collected from ciona embryos at the gastrula and larval stages, using the mirtrap computational program [], a method that makes no hypothesis on the evolutionary conservation of these candidates. of these 348 mirnas, only 47 mirnas, belonging to 36 families, were widely […]

PMCID: 5428504
PMID: 28381865
DOI: 10.1038/s41598-017-00488-y

[…] potential target porcine mrnas for zma-mir164a-5p that had a low minimum free energy value (mfe< −25 kcal·mol−1) and for which the seed region was highly matched (supplementary table ). next, the mirtrap system, an rna-induced silencing complex trap method, , was used to isolate specific mirna target genes in a porcine kidney cell line (pk15). as shown in fig. , of 15 potential zma-mir164a-5p […]


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miRTRAP institution(s)
Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA, USA
miRTRAP funding source(s)
This work was supported by NIH grant 5R24GM075049-04.

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