Beacon Designer protocols

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Beacon Designer specifications


Unique identifier OMICS_15903
Name Beacon Designer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Mac OS, Windows
Computer skills Medium
Stability Stable
Maintained Yes



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Beacon Designer in pipelines

PMCID: 5786550
PMID: 29403517
DOI: 10.3389/fpls.2018.00007

[…] et al., )., quantitative real-time rt-pcr (qrt-pcr) analysis was performed to validate the rna-seq results. twelve degs were randomly selected for qrt-pcr. all primers were designed using the beacon designer software (version 7.9) (additional file: table ). the housekeeping gene tubulin (genbank accession go264294) was used as an internal standard (chi et al., ). total rna (1 μg) was used […]

PMCID: 5845112
PMID: 29556202
DOI: 10.3389/fphys.2018.00158

[…] were used as the endogenous control to normalize the target gene expression and correct for any sample-to-sample variation. the primers (table ) of the target and reference genes were designed by beacon designer 7 (premier biosoft international). the specificity of each primer set was validated by melt-curve analysis, and the efficiency was calculated by analyzing standard curves […]

PMCID: 5928209
PMID: 29740343
DOI: 10.3389/fphys.2018.00432

[…] nanjing, china) as the manufacturer's instructions. briefly, the reaction programs were 10 min at 95°c, 40 cycles of 95°c for 15 s and 60°c for 1 min. the qpcr primers (table ) were designed using beacon designer 7.9 (premier biosoft international, ca, usa). then, the relative expression levels of sexigrs mrna were calculated based on the ct-values of target gene and two reference genes […]

PMCID: 5232348
PMID: 28081263
DOI: 10.1371/journal.pone.0170072

[…] 1000 bootstrap replicates []., the qpcr was performed in a mastercycler ep realplex (eppendorf, hamburg, germany) with gene specific primers () designed based on pameobp nucleotide sequences using beacon designer 7.7. p. americana actin mrna (aam77467) and adp-ribosylation factor were used as reference genes [, ]. the expression levels of the tested mrnas were measured using gotaq qpcr master […]

PMCID: 5247736
PMID: 28106122
DOI: 10.1038/srep41040

[…] gse74544., for verification of transcriptome data, qpcr was performed by lightcycler 480 system (roche, germany) with 2 × sybr premix ex taq (takara, dalian, china). the primers were designed by beacon designer 7 and the sequences were listed in ., as the major genes of central metabolism were identified by transcriptome, these genes’ expression levels of h915-1 at 48 h and a1 at 60 h […]

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Beacon Designer in publications

PMCID: 5945592
PMID: 29748620
DOI: 10.1038/s41598-018-25684-2

[…] with the high capacity cdna reverse transcription kit (applied biosystems, foster city, ca, usa). for the quantitative rt-pcr in organotypic rat hippocampal slices, primers were designed using the beacon designer 4.2 software (premier biosoft international, palo alto, ca, usa) on rat sequences available in genbank (table ). the reaction was performed in a final volume of 15 μl in an iq5 […]

PMCID: 5935387
PMID: 29727440
DOI: 10.1371/journal.pone.0193831

[…] ca, usa). total rna of the whole insect was extracted by using trizol reagent (invitrogen)., gene-specific primers () were designed using primer3 web (version 4.0.0) ( and beacon designer 7.90, and the cdna was prepared according to the instruction. the s. furcifera housekeeping gene ribosomal protein l9 (genebank accession number kp735523) and ribosomal protein l10 […]

PMCID: 5937831
PMID: 29690862
DOI: 10.1186/s12864-018-4678-x

[…] step one ™ real-time pcr system (applied biosystems, singapore) using the super real fluorescence quantification kit (sybr green) (fp205, tiangen, china). the target gene primers were designed by beacon designer 7.9. the cucumber actin gene was used as an internal reference to normalize the qrt-pcr data., all reactions were carried out according to the manufacturer’s instructions and repeated […]

PMCID: 5924566
PMID: 29690608
DOI: 10.3390/genes9040224

[…] tip green qpcr supermix (transgen biotech, beijing, china). according to a previous workflow, the normalization of each reaction threshold cycle (ct) value was determined by pear tubulin gene [,]. beacon designer v7.9 was used to design specific primers of the qrt-pcr analysis [,], which are presented in . all expression data were obtained from three biological repeats. the spss v19.0 software […]

PMCID: 5903143
PMID: 29686777
DOI: 10.5487/TR.2018.34.2.151

[…] biosystems, fostercity, ca, usa), according to the manufacturer’s instructions. for detection of target gene transcripts, we designed specific forward and reverse oligonucleotide primers using beacon designer software (premier biosoft, palo alto, ca, usa). the primer sequences are listed in . target mrna levels were normalized using glyceraldehyde 3-phosphate dehydrogenase (gapdh) […]

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