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sRNAbench specifications

Information


Unique identifier OMICS_29052
Name sRNAbench
Alternative name miRanalyzer
Interface Web user interface
Restrictions to use None
Biological technology Illumina
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Michael Hackenberg
  • person_outline Danijela Koppers-Lalic

Information


Unique identifier OMICS_29052
Name sRNAbench
Alternative name miRanalyzer
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Michael Hackenberg
  • person_outline Danijela Koppers-Lalic

Publications for sRNAbench

sRNAbench citations

 (56)
call_split

Comprehensive analysis of blood cells and plasma identifies tissue specific miRNAs as potential novel circulating biomarkers in cattle

2018
BMC Genomics
PMCID: 5894187
PMID: 29636028
DOI: 10.1186/s12864-018-4646-5
call_split See protocol

[…] e HiSeq 2000 Sequencing System (Illumina). Small RNA libraries were prepared using 5 μL of RNA extract. Raw sequencing data, available on the GEO database (Accession GSE84871 []), were analysed using sRNAbench 1.0 [, ]. Briefly, the software was run in genome mode using default settings, with the bovine genome (bosTau4) and miRBase 21 as reference (accessed on 30 April 2015 [, ]) in order to ident […]

call_split

Glycosylated extracellular vesicles released by glioblastoma cells are decorated by CCL18 allowing for cellular uptake via chemokine receptor CCR8

2018
J Extracell Vesicles
PMCID: 5912193
PMID: 29696074
DOI: 10.1080/20013078.2018.1446660
call_split See protocol

[…] facturer (Illumina). RNAseq was performed on a HiSeq 2500 (Illumina) pair-end 125 nucleotide length read, using equimolar amounts for each sample. Sequencing reads analysis was performed by using the sRNAbench analysis package as described previously []. Briefly after adaptor trimming and unique reads grouping, reads were aligned to the human genome (UCSC hg19) using the Bowtie 1.1.2. To provide a […]

library_books

Malaria infected red blood cells release small regulatory RNAs through extracellular vesicles

2018
Sci Rep
PMCID: 5772623
PMID: 29343745
DOI: 10.1038/s41598-018-19149-9

[…] n was cultured in RBCs of three different donors.Small RNA sequencing of the EV libraries yielded a total of 83’319’134 raw reads that were pre-processed and trimmed to remove adapter sequences using sRNAbench to identify high quality reads that were considered for further analysis. After processing for adapter and unmapped sequences, the number of reads was reduced to 26’647’563, 8’126’655 and 11 […]

library_books

miRNome Profiling in Bicuspid Aortic Valve Associated Aortopathy by Next Generation Sequencing

2017
Int J Mol Sci
PMCID: 5713463
PMID: 29165337
DOI: 10.3390/ijms18112498

[…] ressed when showing an absolute fold change (FC) of 1.5 or greater between BAV and TAV patients, with an FDR-adjusted p-value ≤ 0.05.The prediction of novel human microRNAs was performed in iMir with miRanalyzer and miRDeep 2 stand-alone tools. In order to predict the orthology relationships among organisms, the novel identified mature miRNAs were aligned to mature miRNA sequences deposited in miR […]

library_books

Non coding RNAs and Their Roles in Stress Response in Plants

2017
PMCID: 5673675
PMID: 29017967
DOI: 10.1016/j.gpb.2017.01.007

[…] . Recently, with the advent of high-throughput sequencing, several computational tools have been established to identify and predict miRNAs ().According to sRNA sequencing (sRNA-seq) data, miRPlant , miRanalyzer , miRA and miRDeep-P could be used to predict new miRNAs; whereas based on target data, Semirna could be used to search for miRNAs.A great number of programs and algorithms have been ap […]

library_books

The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading

2017
Genome Biol
PMCID: 5634881
PMID: 29017520
DOI: 10.1186/s13059-017-1321-0

[…] conditions (i.e., Ct-ERβ EF/wild-type EF) ≥ 2 or showing a negative EF in wild-type IPβ vs input were selected. The different classes of small RNAs obtained in IPβ in Ct-ERβ cells were assessed using sRNABench []. Classification of enriched RNAs was performed using the "Gene biotype" term in ENSEMBL using a.gtf file downloaded from Genecode (http://www.gencodegenes.org/#). […]

Citations

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sRNAbench institution(s)
Department of Genetics, University of Granada, Campus de Fuentenueva, Granada, Spain; Bioinformatics Group, Biomedical Research Center (CIBM), Granada, Spain; Genomics and Bioinformatics Platform of Andalusia (GBPA), Edificio INSUR, Sevilla, Spain; Biology Centre, Academy of Sciences of Czech Republic, Budweis, Czech Republic; Australian Centre for Plant Functional Genomics, the University of Adelaide, Adelaide, SA, Australia; Department of Pathology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands
sRNAbench funding source(s)
Supported by the Spanish Government (FIS2012-36282) and Basque country ‘AE’ grant.

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