Journal: Database: The Journal of Biological Databases and Curation

Article Title: GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR

doi: 10.1093/database/bar040

Figure Lengend Snippet: JBrowse-based graphical view of GETPrime primer pairs targeting the Rbbp9 mouse gene. The blue boxes on the left are the available tracks that can be dragged in the JBrowse genome view . In this example, the transcripts, the gene-specific primers (covering the majority of splice variants if possible) and the transcript-specific primers (covering a single splice variant, when possible) have been dragged into the browser. The upper part of the figure shows tools to zoom, to move to up- or downstream of the genome location, and to enter another chromosome, another position on the chromosome or also an Ensembl ID. Each primer is annotated by its Ensembl ID, its iteration in GETPrime (e.g. −1), its ranking (e.g. _3) and its primer type (forward and reverse primers are abbreviated Fwd and Rv, respectively). The blue box for each primer represents the respective alignment to the transcripts and sometimes a thin line between two blue boxes is used to bridge an intron region for primers spanning two exons. The primer pairs in the gene-specific track cover both transcripts. The primer pairs from the first iteration (‘−1’) and the second iteration (‘−2’) in the transcript-specific track are specific to the largest transcript Rbbp9-001 and the shortest transcript Rbbp9-002 , respectively.

Article Snippet: To fill this current void, we developed our own qPCR primer design software, GETPrime.

Techniques: Variant Assay

Journal: Database: The Journal of Biological Databases and Curation

Article Title: GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR

doi: 10.1093/database/bar040

Figure Lengend Snippet: Graphical view and qPCR results to validate Ubtf -targeting primers covering either all or a subset of Ubtf transcripts. ( A ) The ‘Ubtf’ primer pair in blue covers all seven transcripts (gene-specific primers) and the red ‘Ubtf_a’ and ‘Ubtf_b’ primer pairs cover five and two transcripts, respectively (transcript-specific primers). In this example, GETPrime could not find primers differentiating each transcript. ( B ) The relative gene expression levels before differentiation (D0) and four days after (D4) were normalized to Hprt1 and Tubb2c expression levels. ‘Ubtf’ represents the primer pair covering all seven transcripts, whereas, ‘Ubtf_a’ and ‘Ubtf_b’ are primer pairs specific to a subset of five and two transcripts, respectively. ‘Ubtf_a+Ubtf_b’ represents the sum of relative gene expression of ‘Ubtf_a’ and ‘Ubtf_b’. The data indicate that GETPrime can effectively differentiate distinct transcripts, as the sum of the individual transcript amounts matched the overall gene expression amount.

Article Snippet: To fill this current void, we developed our own qPCR primer design software, GETPrime.

Techniques: Gene Expression, Expressing

Journal:

Article Title: Expression of prostanoid receptors in human ductus arteriosus

doi: 10.1038/sj.bjp.0705092

Figure Lengend Snippet: Primer design for PCR amplification of prostanoid receptors and β-actin

Article Snippet: Abundance of receptor mRNA was expressed relative to β-actin mRNA. table ft1 table-wrap mode="anchored" t5 caption a7 Primer design for PCR amplification of prostanoid receptors and β -actin Open in a separate window

Techniques: Amplification

Journal:

Article Title: Expression of prostanoid receptors in human ductus arteriosus

doi: 10.1038/sj.bjp.0705092

Figure Lengend Snippet: Expression of prostanoid receptor mRNA in human DA. RNA was isolated from excised tissue, reverse-transcribed by oligo(dT) and PCR amplification for all tissue samples was repeated three times. A fragment of β-actin was amplified as internal control. A representative expression pattern of one tissue sample is shown, base pair markers (bp) are indicated on both sides.

Article Snippet: Abundance of receptor mRNA was expressed relative to β-actin mRNA. table ft1 table-wrap mode="anchored" t5 caption a7 Primer design for PCR amplification of prostanoid receptors and β -actin Open in a separate window

Techniques: Expressing, Isolation, Reverse Transcription, Amplification, Control

Journal:

Article Title: Expression of prostanoid receptors in human ductus arteriosus

doi: 10.1038/sj.bjp.0705092

Figure Lengend Snippet: Expression of the different prostanoid receptors relative to the expression of β-actin. RNA was isolated from excised tissue, reverse-transcribed by oligo(dT) and PCR amplification was performed for the indicated prostanoid receptors. Intensity of DNA bands is presented as percentage of amplification of β-actin fragment.

Article Snippet: Abundance of receptor mRNA was expressed relative to β-actin mRNA. table ft1 table-wrap mode="anchored" t5 caption a7 Primer design for PCR amplification of prostanoid receptors and β -actin Open in a separate window

Techniques: Expressing, Isolation, Reverse Transcription, Amplification