tm instrument  (fluidigm)

Journal: BMC Genomics

Article Title: A duck RH panel and its potential for assisting NGS genome assembly

doi: 10.1186/1471-2164-13-513

Figure Lengend Snippet: Estimations of duck genome retention in the RH clones. A: retention frequencies of thirty-one microsatellite markers and four scaffold markers before (white) and after (grey) whole genome amplification. The test was done on the 90 selected hybrids by conventional Agarose genotyping. The expected chromosome locations of the markers (given in brackets) are derived from the chicken/duck comparative FISH mapping and a duck genetic map (Marie-Etancelin et al., in prep) for the microsatellite markers and according to comparative genomic data given by the Narcisse software for the scaffold markers. B : Retention frequencies of thirty-nine scaffolds markers obtained using three different genotyping strategies. The thirty-nine scaffold markers were genotyped using either (i) the amplified panel with conventional agarose genotyping (blue: WGA-PCR), (ii) the non amplified panel and genotyping with the Fluidigm BioMark gene expression dynamic array (green: Pre-ampFLDMqPCR) or (iii) the amplified panel and genotyping with the Fluidigm BioMark TM IFC Dynamic Array TM genotyping by quantitative PCR without any pre-amplification step (purple: WGA-FLDMqPCR). The markers are distributed along the X axis from the lowest to the highest retention frequencies obtained by the first method (the amplified panel with conventional agarose genotyping WGA-PCR in blue).

Article Snippet: In our case, by performing qPCR with the Fluidigm BioMark TM IFC Dynamic Array TM genotyping, the additional benefit is high throughput, as the identification of bands on gel electrophoresis is replaced by monitoring the PCR with Ct (Cycle threshold) and end point Tm (melting temperature) values, allowing the distinction between specific and non-specific amplification profiles.

Techniques: Clone Assay, Whole Genome Amplification, Derivative Assay, Software, Amplification, Expressing, Real-time Polymerase Chain Reaction

Journal: BMC Genomics

Article Title: A duck RH panel and its potential for assisting NGS genome assembly

doi: 10.1186/1471-2164-13-513

Figure Lengend Snippet: Genotyping by Fluidigm BioMarkTM IFC Dynamic ArrayTM quantitative PCR. (A) WGA-FLDMqPCR: WGA-amplified DNA and qPCR. Left: double-strand DNA (dsDNA) accumulation curve as a function of the number of cycles. Right: melting curve of the final product. Green: positive control (duck DNA). Red: a hybrid which was positive (containing duck DNA corresponding to the marker tested). Blue: a negative hybrid. Yellow: negative control (hamster DNA). (B) Pre-ampFLDMqPCR: non-amplified DNA, a pre-amplification step with a mix of the 96 primer pairs for the 96 markers tested in the Fluidigm BioMarkTM assay and qPCR. The same markers and controls are used as in (A) . The sensitivity is higher in (B) , with a lower number of cycles necessary for detection of duck DNA. The negative control and the hybrid not containing duck DNA amplify at a much higher number of cycles and the non-specific products amplified can easily be distinguished by their different melting temperature values (right). In both experiments, no amplification was obtained from water (data not shown).

Article Snippet: In our case, by performing qPCR with the Fluidigm BioMark TM IFC Dynamic Array TM genotyping, the additional benefit is high throughput, as the identification of bands on gel electrophoresis is replaced by monitoring the PCR with Ct (Cycle threshold) and end point Tm (melting temperature) values, allowing the distinction between specific and non-specific amplification profiles.

Techniques: Real-time Polymerase Chain Reaction, Amplification, Positive Control, Marker, Negative Control

Journal: BMC Genomics

Article Title: A duck RH panel and its potential for assisting NGS genome assembly

doi: 10.1186/1471-2164-13-513

Figure Lengend Snippet: Genotyping 8 no hit markers using three different genotyping strategies

Article Snippet: In our case, by performing qPCR with the Fluidigm BioMark TM IFC Dynamic Array TM genotyping, the additional benefit is high throughput, as the identification of bands on gel electrophoresis is replaced by monitoring the PCR with Ct (Cycle threshold) and end point Tm (melting temperature) values, allowing the distinction between specific and non-specific amplification profiles.

Techniques:

Journal: BMC Genomics

Article Title: A duck RH panel and its potential for assisting NGS genome assembly

doi: 10.1186/1471-2164-13-513

Figure Lengend Snippet: Comparison of marker retention with the three genotyping techniques

Article Snippet: In our case, by performing qPCR with the Fluidigm BioMark TM IFC Dynamic Array TM genotyping, the additional benefit is high throughput, as the identification of bands on gel electrophoresis is replaced by monitoring the PCR with Ct (Cycle threshold) and end point Tm (melting temperature) values, allowing the distinction between specific and non-specific amplification profiles.

Techniques: Marker