miRge protocols

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miRge specifications

Information


Unique identifier OMICS_10762
Name miRge
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Requirements
Cutadapt, Bowtie, PERL GD
Maintained Yes

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Maintainer


  • person_outline Marc Halushka <>

Publications for miRge

miRge in pipeline

2017
PMCID: 5430826
PMID: 28439113
DOI: 10.1038/s41598-017-01167-8

[…] (santa clara, ca). libraries were sequenced (single end reads) on the illumina hiseq2500 (illumina, san diego, ca) to generate 50 million reads/sample. mirna reads were aligned and mapped using mirge, and summarized at the raw reads level using the following components: cutadapt for sequence read filtering and adapter trimming, and bowtie for sequence read alignment to known mature human […]


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miRge in publications

 (3)
PMCID: 5748684
PMID: 29206165
DOI: 10.3390/genes8120366

[…] of the positive transcription elongation factor p-tefb []., many mirna processing pipelines have been established for utilizing hts data. the major pipelines include: oasis [], chimira [], mirge [], and tiger [], etc. several tools have also been developed to detect isomirs such as seqbuster [], isomirid [] and deanniso []. one trna detection tool, tdrmapper [], is currently available. […]

PMCID: 5693599
PMID: 29176936
DOI: 10.1186/s12935-017-0474-y

[…] the quality and concentration of rna was assessed using a nanodrop spectrophotometer (thermo-scientific, wilmington, del)., expression of the selected mir-33a, pd-1, pd-l1 and ctla4 genes among a mirge panel was measured using the nanostring ncounter technology (nanostring technologies, seattle, wa). the ncounter measures total counts of mrnas/mirna by a multiplex hybridization assay followed […]

PMCID: 4725739
PMID: 26808438
DOI: 10.1371/journal.pone.0147411

[…] microrna-adapted shrna based on optimized mirna mimic design (.) []. we transduced viral vectors in 832/13 cells to establish inducible cell lines harboring chrebpβ shrna targeting sequence (mirge-β cells) and non-silencing sequence (mirge-n cells). the expression of chrebpβ in induced mirge-β cells was ~46% as compared to expression in induced mirge-n cells (.). however, rgs16 […]


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miRge institution(s)
Department of Pathology, Johns Hopkins University SOM, Baltimore, MD, USA
miRge funding source(s)
Supported by the National Institutes of Health [1R01HL137811] and the American Heart Association [Grant-in-Aid 17GRNT33670405].

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