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Protocols

RDML specifications

Information


Unique identifier OMICS_20822
Name RDML
Alternative name real-time PCR data markup language
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Konstantin Blagodatskikh

Additional information


A web application is available at: http://shtest.evrogen.net/rdmlEdit/

Information


Unique identifier OMICS_20822
Name RDML
Alternative name real-time PCR data markup language
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Medium
Version 0.9.8
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Konstantin Blagodatskikh

Additional information


A web application is available at: http://shtest.evrogen.net/rdmlEdit/

Publications for real-time PCR data markup language

RDML citations

 (25)
library_books

rdml: A Mathematica package for parsing and importing Real Time qPCR data

2017
BMC Res Notes
PMCID: 5469176
PMID: 28606167
DOI: 10.1186/s13104-017-2533-9

[…] The rdml package, as well as input example files, are freely available at https://github.com/ramiromagno/rdml. […]

call_split

Evaluation of Reference Genes for Normalization of Gene Expression Using Quantitative RT PCR under Aluminum, Cadmium, and Heat Stresses in Soybean

2017
PLoS One
PMCID: 5207429
PMID: 28046130
DOI: 10.1371/journal.pone.0168965
call_split See protocol

[…] IQE (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) guidelines proposed the use of quantification cycle (Cq) value over the threshold cycle (Ct) according to the RDML (Real-Time PCR Data Markup Language) data standard []. Cq value represents the number of cycles when the density of fluorescence meets the set threshold. Therefore, Cq values were used in this study. E […]

library_books

Vitellogenin knockdown strongly affects cotton boll weevil egg viability but not the number of eggs laid by females

2016
PMCID: 4936639
PMID: 27419079
DOI: 10.1016/j.mgene.2016.06.005

[…] rmined as the number of cycles required to reach a fixed threshold in the exponential phase of PCR. The number of cycles was referred to as the Cq value (Quantification Cycle), in accordance with the RDML standards (). The efficiency of each primer for each reaction and Cq value were calculated individually by using the qPCR miner software (www.miner.ewindup.info) (). The relative expression of Vi […]

library_books

Normalization for Relative Quantification of mRNA and microRNA in Soybean Exposed to Various Abiotic Stresses

2016
PLoS One
PMCID: 4866712
PMID: 27176476
DOI: 10.1371/journal.pone.0155606

[…] orm and interpret RT-qPCR experiments. Many technical defects can affect the accuracy of RT-qPCR analysis. Therefore, the minimum information required to publish RT-qPCR experiments (MIQE) [] and the Real-Time PCR Data Markup Language (RDML) were published[]. These standards for RT-qPCR experiments focus on the reliability and consistency of results. According to the MIQE, the selection of suitabl […]

library_books

Inter population Differences in Retrogene Loss and Expression in Humans

2015
PLoS Genet
PMCID: 4608704
PMID: 26474060
DOI: 10.1371/journal.pgen.1005579

[…] eal-Time PCR Software v1.0 (Applied Biosystems). The cut-off value for Ct (cycle threshold) was established as 32, based on previously published studies []. Additionally, results were exported into a RDML data format [] and used for PCR efficiency estimation using LinRegPCR software []. An efficiency value over 1.8 was obtained for all retrogenes and considered as acceptable. The relative amount o […]

library_books

Associations of circulating plasma microRNAs with age, body mass index and sex in a population based study

2015
BMC Med Genomics
PMCID: 4604724
PMID: 26462558
DOI: 10.1186/s12920-015-0136-7

[…] aw data were processed using SDS 2.4 (Applied Biosystems) to assign the baseline and threshold for Ct (threshold cycle: the PCR cycle at which the target is quantified in a given sample, according to Real-time PCR Data Markup Language (RDML) guidelines []) determination. To determine the technical variation between the Exiqon Serum/Plasma Focus microRNA PCR Panel plates, the inter-plate calibrator […]

Citations

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RDML institution(s)
Institute of Biotechnology, Brandenburg University of Technology Cottbus–Senftenberg, Senftenberg, Germany; Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland; Department of Andrology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Evrogen JSC, Moscow, Russia
RDML funding source(s)
Supported by the Federal Ministry of Education and Research (BMBF) InnoProfile-Transfer-Projekt 03IPT611X and in part by ‘digilog: Digitale und analoge Begleiter fur eine alternde Bevolkerung’ (Gesundheitscampus Brandenburg, Brandenburg Ministry for Science, Research and Culture).

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