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RNAxs specifications

Information


Unique identifier OMICS_08701
Name RNAxs
Interface Web user interface
Restrictions to use None
Input data Sequence
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Hakim Tafer <>

Publication for RNAxs

RNAxs in publications

 (11)
PMCID: 5826319
PMID: 29515371
DOI: 10.3389/fnmol.2018.00052

[…] had to be fixed with 0.5% glutaraldehyde in pbs for 20 min., retinae from mice of the c57 bl6 j strain (adult, 2–3 months) were dissected in sterile pbs. the “total rna isolation kit nucleo spin rnaxs” (macherey-nagel, düren, germany) was used to isolate rna. rna concentration was measured via nanodrop and 1 μg of rna was dnase treated. samples for cdna synthesis were prepared: 1 μl […]

PMCID: 5933895
PMID: 29223142
DOI: 10.4062/biomolther.2017.115

[…] therapeutics, we designed a melanin sirna pool by applying multiple prediction programs to reduce human tyrosinase levels. first, 272 sirnas passed the target accessibility evaluation using the rnaxs program. then we selected 34 sirna sequences with δg ≥−34.6 kcal/mol, i-score value ≥65, and sirna scales score ≤30. sirnas were designed as 19-bp rna duplexes with an asymmetric 3′ overhang […]

PMCID: 5094585
PMID: 27812135
DOI: 10.1371/journal.pone.0165420

[…] experiments. 70 percent or more of target mrna inhibition was considered as a successful sirna experiment., rna was extracted 24h after treatment with mdp and/or lps with the mascherey-nagel rnaxs kit. customized pcr arrays (sabiosciences) were performed and analyzed by tebu-bio (france). two housekeeping genes, gapdh and tbp were used to analyse the expression rate of the genes […]

PMCID: 5097791
PMID: 27843938
DOI: 10.1155/2016/2048987

[…] dead cells were excluded from the analysis by staining with 4′,6-diamidino-2-phenylindole (dapi: sigma)., total rna was isolated from mast cells by using rnaiso plus reagent (takara) and nucleospin rnaxs (takara). the cdna was synthesized using superscript vilo cdna synthesis kit (life technologies), and semiquantitative pcr was then performed using takara ex taq hs dna polymerase (takara). […]

PMCID: 4956106
PMID: 27441640
DOI: 10.1371/journal.pone.0159211

[…] []. we selected sirnas with high threshold scores and ones that mapped to 90% inhibition of viral transcripts. we then performed expression rate analysis for their target accessibility using the rnaxs tool []. sirnas targeting accessible regions of the ires (loop structures) either at the 5’ or 3’ ends of the sirna were then selected. sirnas that mainly targeted the ires stem base pairs […]


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RNAxs institution(s)
Institute of Theoretical Biochemistry (TBI), University of Vienna, Austria

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