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Protocols

miRBase specifications

Information


Unique identifier OMICS_02808
Name miRBase
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Content license CC Zero
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/MiRBase

Maintainers


  • person_outline miRBase Team
  • person_outline Sam Griffiths-Jones

Publications for miRBase

miRBase citations

 (1625)
call_split

Distinguishing mirtrons from canonical miRNAs with data exploration and machine learning methods

2018
Sci Rep
PMCID: 5953923
PMID: 29765080
DOI: 10.1038/s41598-018-25578-3
call_split See protocol

[…] In the study we used two datasets. First, the miRBase set (Supplementary Table ) consisted of mirtrons and canonical miRNAs deposited in miRBase (Release 21, 06/14). To date Wen et al. provided the most comprehensive but also stringent mirtron/ca […]

library_books

A deeper view into the significance of simple sequence repeats in pre miRNAs provides clues for its possible roles in determining the function of microRNAs

2018
BMC Genet
PMCID: 5941480
PMID: 29739315
DOI: 10.1186/s12863-018-0615-x

[…] The SSRIT analysis of all the available miRNA precursors extracted from miRBase showed significant presence of SSRs which accounted to about 29.8%. The frequency and distribution pattern of SSRs varied extensively across different taxa analysed (see Additional file ). SSR […]

library_books

Evaluation of commercially available small RNASeq library preparation kits using low input RNA

2018
BMC Genomics
PMCID: 5936030
PMID: 29728066
DOI: 10.1186/s12864-018-4726-6

[…] ranscriptome. Also, the reads that are not mapped to the human genome are mapped to the human transcriptome, The library for the human transcriptome is built by concatenating miRNAs and hairpins from miRBase 21 [], tRNAs from gtRNAdb [], piRNAs from piRBase v1.0 [], protein-coding, non-coding and and other RNA sequences from ENSEMBL 75. The STAR alignment is performed end to end with a single mism […]

library_books

Cigarette smoke and chewing tobacco alter expression of different sets of miRNAs in oral keratinocytes

2018
Sci Rep
PMCID: 5935709
PMID: 29728663
DOI: 10.1038/s41598-018-25498-2

[…] ce databases (GtRNA, piRNA, Rfam& snoRNA)– using Bowtie (version 1.1.2). Remaining reads were used for known miRNA identification. These reads were first aligned to mature and precursor sequence from miRBase 21 miRNA database (Human) using Bowtie. Unaligned reads were further aligned against human genome hg19 using miRDeep2 (version 2.0.0.6). Known miRNA that are quantified with at least 10 reads […]

library_books

Robust Sub nanomolar Library Preparation for High Throughput Next Generation Sequencing

2018
BMC Genomics
PMCID: 5935984
PMID: 29728062
DOI: 10.1186/s12864-018-4677-y

[…] First, Cutadapt 1.9.1 was used to trim Illumina TruSeq adapter sequences from fastq files at 3′ ends. Subsequently, for microRNA, miRDeep2 v.2.0.0.7 was used to map the reads to the miRBase (version 21) microRNA database and quantify microRNA expression levels. For other small noncoding RNA, data were analyzed using Qiagen (Germantown, MD) CLC Genomics Workbench 8.5.1 for mapping […]

library_books

An integrated view of the role of miR 130b/301b miRNA cluster in prostate cancer

2018
PMCID: 5930504
PMID: 29744254
DOI: 10.1186/s40164-018-0102-0

[…] tracted from the original article. Martens-Uzunova et al. RNA-seq data [] was provided by the authors; it was normalized, counted and annotated using miRDeep2 software using default parameters [] and miRBase database Release 21. The small RNA-seq data from the TCGA-PRAD was retrieved as explained in the next section. […]

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miRBase institution(s)
School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
miRBase funding source(s)
Supported by Biotechnology and Biological Sciences Research Council [BB/G022623/1].

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