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piRNABank specifications

Information


Unique identifier OMICS_04870
Name piRNABank
Restrictions to use Academic or non-commercial use
Version 2.0
Maintained Yes

Taxon


  • Invertebrates
    • Drosophila melanogaster
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus

Maintainer


  • person_outline Shipra Agrawal

Publication for piRNABank

piRNABank citations

 (39)
library_books

Alterations in sperm DNA methylation, non coding RNA expression, and histone retention mediate vinclozolin induced epigenetic transgenerational inheritance of disease

2018
PMCID: 5920293
PMID: 29732173
DOI: 10.1093/eep/dvy010

[…] ads shorter than 15 nt were discarded by Cutadapt []. The remaining reads were matched to known rat sncRNA, consisting of mature miRNA (miRBase, release 21), tRNA (Genomic tRNA Database, rn5), piRNA (piRNABank), 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 DES […]

library_books

Differentially expressed microRNAs between cattleyak and yak testis

2018
Sci Rep
PMCID: 5766512
PMID: 29330490
DOI: 10.1038/s41598-017-18607-0

[…] raries were matched to the latest Sanger miRBase (http://www.mirbase.org/) and other noncoding databases like ncRNA (http://asia.ensembl.org/index.html), piRNA (http://www.ncbi.nlm.nih.gov/and http://pirnabank.ibab.ac.in/) and Rfam database (http://rfam.sanger.ac.uk/) with a tolerance of two mismatches using the software of CLC genomics_workbench 5.5. Sequences that did not overlap with any annota […]

library_books

Characterization and selective incorporation of small non coding RNAs in non small cell lung cancer extracellular vesicles

2018
PMCID: 5763536
PMID: 29344346
DOI: 10.1186/s13578-018-0202-x

[…] ligned reads were categorized and annotated to known non-coding small RNA transcripts using Rfam version 11.0 [] for YRNA, rRNA, snRNA, snoRNA, and tRNA. miRBase version 21 [] was used for miRNA, and piRNABank [] was used for piRNA.Next, the quantity of small RNA in each sample was obtained and normalized as RPM (number of mapped reads per million clean reads). The clean reads of miRNA, containing […]

library_books

Non coding RNAs predict recurrence free survival of patients with hypoxic tumours

2018
Sci Rep
PMCID: 5760628
PMID: 29317756
DOI: 10.1038/s41598-017-18462-z

[…] f mismatches < = 5% of mapped length, and iii) splicing switched off. Mapped reads were subsequently quantified within the PartekFlow™ platform using a piRNA-specific annotation file generated by the piRNABank (http://pirnabank.ibab.ac.in/). This reference transcriptome considers widely accepted piRNA sequence features, such as sequence bias for uracil in the 1st and adenine in the 10th position, […]

library_books

Small RNA profiling for identification of miRNAs involved in regulation of saponins biosynthesis in Chlorophytum borivilianum

2017
BMC Plant Biol
PMCID: 5745966
PMID: 29281971
DOI: 10.1186/s12870-017-1214-0

[…] core. Raw reads were then processed and 5′ and 3′ adapter sequences were eliminated using Cutadapt tool (v-1.3) []. Remaining reads were then aligned against a number of databases like GtRNAdb, Rfam, piRNABank, siRNAdb, NCBI Genbank, deepBase to eliminate other non-coding RNAs like tRNA, rRNA, piRNA, siRNA, snRNA, and snoRNA, respectively using Bowtie2 program (version 2.1.0) []. The remaining rea […]

call_split

A comprehensive profile of circulating RNAs in human serum

2017
RNA Biol
PMCID: 5798962
PMID: 29219730
DOI: 10.1080/15476286.2017.1403003
call_split See protocol

[…] nerated by FASTX v0.14) to the human genome (hg38) using Bowtie2 v2.2.9 (10 alignments per read were allowed). We compiled a comprehensive annotation set from miRBase/MirGeneDB [] for miRNAs, pirBAse/pirnabank for piRNAs [], GENCODE [] for other RNAs and tRNAs. We used SeqBuster [] to get isomiR and miRNA profiles of our samples. To count the reads mapped on other RNAs, HTSeq [] was utilized in a […]

Citations

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piRNABank institution(s)
Institute of Bioinformatics and Applied Biotechnology, Bangalore, India

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