Journal: Cell Reports

Article Title: Genetic Predisposition to Chronic Lymphocytic Leukemia Is Mediated by a BMF Super-Enhancer Polymorphism

doi: 10.1016/j.celrep.2016.07.053

Figure Lengend Snippet: Contact Profile of the BMF 4C Viewpoint in Combination with ChIP-Seq Data (A) Heatmap representing chromatin interactions in GM12878 cells at 40.32–40.52 Mb on chromosome 15. Chromatin contact domains called by the Arrowhead algorithm are marked by white lines ( Rao et al., 2014 ). The contact domain and CD19 + B cell super-enhancer ( Hnisz et al., 2013 ) encompassing rs539846 are labeled in pink and yellow, respectively. (B) 4C-seq analyses in MEC1 CLL cells indicate the formation of a loop domain between rs539846 and cis -regulatory elements. The 4C viewpoint (green box) lies adjacent to rs539846 (dotted line). A 10-kb masked region (gray box) is also marked. ENCODE ChIP-seq data from GM12878 cells show the correspondence between loop formation and CTCF and RELA transcription factor occupancy. Canonical transcripts and chromosome 15 position also are shown.

Article Snippet: Using 4C primer design software ( http://mnlab.uchicago.edu/4Cpd/ ), we identified a viewpoint adjacent to SNP rs539846.

Techniques: ChIP-sequencing, Labeling

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