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Protocols

piRBase specifications

Information


Unique identifier OMICS_06660
Name piRBase
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Version 2.0
Maintained Yes

Maintainer


  • person_outline Da-Wei Huang

Publications for piRBase

piRBase citations

 (14)
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

[…] 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 mismatch allowed while mapping and each read is allowe […]

library_books

Investigation into the role of the germline epigenome in the transmission of glucocorticoid programmed effects across generations

2018
Genome Biol
PMCID: 5891941
PMID: 29636086
DOI: 10.1186/s13059-018-1422-4

[…] notated sRNA loci were tallied. tRNA and rRNA annotations were obtained from the UCSC table browser. miRNA annotations for rn5 were obtained from Ensembl v78. Rn4 piRNA annotations were obtained from piRBase and converted to rn5 coordinates using CrossMap with the rn4 to rn5 liftover chain file from UCSC. sRNA expression was quantified using FeatureCounts v1.4.6 [] with the following options to di […]

library_books

Alterations in sperm DNA methylation, non coding RNA and histone retention associate with DDT induced epigenetic transgenerational inheritance of disease

2018
PMCID: 5827984
PMID: 29482626
DOI: 10.1186/s13072-018-0178-0

[…] y Cutadapt []. The remaining reads were matched to known rat sncRNA, consisting of mature miRNA (miRBase, release 21), precursor miRNA (miRBase, release 21), tRNA (Genomic tRNA Database, rn5), piRNA (piRBase), rRNA (Ensembl, release 76) and mitochondrial RNA (Ensembl, release 76) using AASRA pipeline with default parameters []. Read counts generated by AASRA were statistically normalized by DESeq2 […]

library_books

Systematic comparison of small RNA library preparation protocols for next generation sequencing

2018
BMC Genomics
PMCID: 5799908
PMID: 29402217
DOI: 10.1186/s12864-018-4491-6

[…] p.shtml (download date July 16, 2015); we only used the mature sequences of Arabidopsis thaliana, Homo sapiens and Brassica napus. For piRNA detection, the reads of the human libraries were mapped to piRBase (http://www.regulatoryrna.org/database/piRNA/; downloaded March 2, 2017). The sampling of the reads was done using seqtk, version 1.0-r31 (H. Li, https://github.com/lh3/seqtk/). Only the reads […]

library_books

Endurance training remodels sperm borne small RNA expression and methylation at neurological gene hotspots

2018
Clin Epigenetics
PMCID: 5785820
PMID: 29416570
DOI: 10.1186/s13148-018-0446-7

[…] res with a false discovery rate less than 0.1 were deemed significant. Human mature miRNAs and their precursor sequences were obtained from miRBase [] version 20. piRNA sequences were downloaded from piRBase version 1.0 []. Human tRNAs were retrieved from UCSC genome browser []. piRNA targets were predicted using piRNAQuest [] which uses sequence similarity to predict piRNA targets. Biotype compos […]

library_books

Effective computational detection of piRNAs using n gram models and support vector machine

2017
BMC Bioinformatics
PMCID: 5751586
PMID: 29297285
DOI: 10.1186/s12859-017-1896-1

[…] he classified families, piRNAdetect incorporates those features to detect piRNAs based on the SVM classifier.In order to train the SVM classifier for piRNA detection, the sequences are drawn from the piRBase [] and Rfam database 12.1 [, ] to construct the datasets with positive samples and negative samples for training and assessment. For each sequence in the positive samples, the sub-sequence wit […]


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piRBase institution(s)
Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; School of Life Sciences, Zhengzhou University, Zhengzhou,China; University of Chinese Academy of Science, Beijing, China; China-UK-NYNU-RRes Joint Laboratory of insect biology, Henan Key Laboratory of Insect Biology in Funiu Mountain, Nanyang Normal University, Nanyang, China
piRBase funding source(s)
Supported by National Key R&D Program of China [2016YFC0901702]; and National Natural Science Foundation of China [31871294].

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