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MiClip specifications


Unique identifier OMICS_06672
Name MiClip
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format SAM, BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


Publication for MiClip

MiClip citations


Emerging Roles of N6 Methyladenosine on HIV 1 RNA Metabolism and Viral Replication

Front Microbiol
PMCID: 5882793
PMID: 29643844
DOI: 10.3389/fmicb.2018.00576

[…] s a 100–200 nt resolution, employed the PA-m6A-seq strategy, which has an improved resolution (around 30 nt) but requires that the m6A site has a nearby site for 4SU incorporation (). The use of the miCLIP strategy (), which has single-nucleotide resolution, will be instrumental in precisely map the m6A sites present along the HIV-1 gRNA.Similar discrepancies arise from the binding sites of YTHDF […]


Multiple functions of m6A RNA methylation in cancer

PMCID: 5870302
PMID: 29587823
DOI: 10.1186/s13045-018-0590-8

[…] not introduce errors during reverse transcription that would allow direct mapping of its position []. A novel method called m6A individual-nucleotide-resolution crosslinking and immunoprecipitation (miCLIP) has marked a major step forward in the field, which augments m6A-seq with UV-induced crosslinking of the antibody to the immunoprecipitated RNA fragments []. Reverse transcription of crosslink […]


Molecular basis for the specific and multivariant recognitions of RNA substrates by human hnRNP A2/B1

Nat Commun
PMCID: 5789076
PMID: 29379020
DOI: 10.1038/s41467-017-02770-z

[…] ligned to the hg19 genome build using bowtie2 according to the source publication. RPM (reads per million mapped reads) was calculated using bedtools.For YTHDC1 binding at m6A sites in HEK293T cells, miCLIP sequencing data (GEO accession number: GSE63753) and YTHDC1 iCLIP data (GEO accession number: GSE78030) were obtained from the GEO database. Sequence alignments were carried out according to th […]


The Dark Side of the Epitranscriptome: Chemical Modifications in Long Non Coding RNAs

Int J Mol Sci
PMCID: 5713356
PMID: 29125541
DOI: 10.3390/ijms18112387

[…] targets of DNMT2 and NSUN2 could be achieved with this method.Indeed, NSUN2-specific methylation sites have been previously identified using yet another m5C detection method called methylation iCLIP (miCLIP) []. This method is derived from individual-nucleotide-resolution cross-linking and immunoprecipitation (iCLIP) [], and abstains from chemical modifications of the RNA. To achieve this, a C271A […]


m6AVar: a database of functional variants involved in m6A modification

Nucleic Acids Res
PMCID: 5753261
PMID: 29036329
DOI: 10.1093/nar/gkx895

[…] essor gene BRCA1 as an example, 102 m6A-associated variants in BRCA1 are presented as a table in the search results page (Figure ). Among them, 11, 26 and 65 m6A-associated variants were derived from miCLIP (high confidence), MeRIP-Seq (medium confidence) and prediction (low confidence), respectively (Figure ). A statistical plot shows the number of germline and somatic m6A-associated variants (Fi […]


The N6 methyladenosine (m6A) forming enzyme METTL3 controls myeloid differentiation of normal and leukemia cells

Nat Med
PMCID: 5677536
PMID: 28920958
DOI: 10.1038/nm.4416

[…] After sequencing, we used the miCLIP pipeline as previously described. In summary, raw miCLIP reads were trimmed of their 3′ adaptor and demultiplexed. Then, PCR-duplicated reads of identical sequences were removed using the pyDup […]

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MiClip institution(s)
Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA

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