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: BMC Genomics

Article Title: Genome-wide identification of the GRF family in sweet orange ( Citrus sinensis ) and functional analysis of the CsGRF04 in response to multiple abiotic stresses

doi: 10.1186/s12864-023-09952-8

Figure Lengend Snippet: Expression profiles of CsGRF s under multiple phytohormone treatments. Expression analysis was carried out in leaves of C . sinensis at different time points (0 h, 3 h, 6 h, 12 h, 24 h and 48 h after treatments). The qPCR results of CsGRFs were normalized by log 2 transform. The heatmap constructed by TBtools software. Color scale erected horizontally at the bottom of the diagram

Article Snippet: The specific primers of CsGRF genes were designed using “Batch qPCR Primer Design” modules of the TBtools software (Version 1.120) [ ] and listed in Supplementary Table S . Realtime qRT-PCR analysis was done using SYBR GREEN PCR Master Mix (TaKaRa, Japan) on a QuantStudio 5 Applied BioSystem (ThermoFisher Scientific, USA) to investigate the expression of CsGRFs after treatments with multiple phytohormones and abiotic stresses in C. sinensis .

Techniques: Expressing, Construct, Software

Journal: BMC Genomics

Article Title: Genome-wide identification of the GRF family in sweet orange ( Citrus sinensis ) and functional analysis of the CsGRF04 in response to multiple abiotic stresses

doi: 10.1186/s12864-023-09952-8

Figure Lengend Snippet: Expression profiles of CsGRF s under multiple abiotic stresses. Expression analysis was carried out in leaves of C . sinensis at different time points (0 h, 3 h, 6 h, 12 h, 24 h and 48 h after NaCl and cold treatments, 0 h, 0.5 h, 1 h, 3 h, 6 h and 12 h after dehydration treatment). The qPCR results of CsGRFs were normalized by log 2 transform. The heatmap constructed by TBtools software. Color scale erected horizontally at the bottom of the diagram

Article Snippet: The specific primers of CsGRF genes were designed using “Batch qPCR Primer Design” modules of the TBtools software (Version 1.120) [ ] and listed in Supplementary Table S . Realtime qRT-PCR analysis was done using SYBR GREEN PCR Master Mix (TaKaRa, Japan) on a QuantStudio 5 Applied BioSystem (ThermoFisher Scientific, USA) to investigate the expression of CsGRFs after treatments with multiple phytohormones and abiotic stresses in C. sinensis .

Techniques: Expressing, Construct, Software