Journal: BMC Bioinformatics

Article Title: Data analysis issues for allele-specific expression using Illumina's GoldenGate assay

doi: 10.1186/1471-2105-11-280

Figure Lengend Snippet: Various plots of the raw signal from GoldenGate arrays measuring ASE . Panels A and B show boxplots of the summarized log 2 ( Cy 5) and log 2 ( Cy 3) intensities respectively from a representative SAM. The data from each array were plotted in a separate boxplot, and color coded by sample (blue - gDNA, red - cDNA). Arrays 4 and 7 have low signal in both channels (IQR ≤ 1) and were excluded from downstream analysis. Density plots for each channel from two typical gDNA and cDNA arrays are presented in panels C and D respectively. These plots also show the systematic difference in overall signal between gDNA and cDNA hybridizations. Smoothed MA -plots for the gDNA (E) and cDNA (F) also highlight the differences. In these plots, a higher density of points is represented by a darker shade of blue.

Article Snippet: The data from a typical cDNA array (Figure ) is more diffuse, with a cluster of points occurring at low intensity, which presumably represents signal from SNPs in transcripts which are either non-expressed, or below the limits of detection using the GoldenGate technology.

Techniques:

Journal: BMC Genomics

Article Title: A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy

doi: 10.1186/1471-2164-13-142

Figure Lengend Snippet: Genotype calling using the Miscanthus GoldenGate™ array . The graphs in panels A-F plot normalized theta (ratio of signal intensities assayed for A and B SNP alleles) against normalized R (signal intensity) for each individual represented as a colored square. Panels A, C, and E illustrate markers that cluster as predicted for a biallelic SNP, which segregate as AA (red), AB (yellow), or BB (blue). Panels B, D, and F illustrate markers that cluster as predicted for a SNP distinguishing alleles for one of two duplicated and unlinked loci, where theta is skewed by the relative dosage of A and B SNPs. In all panels, clusters are defined as sharing alleles with either the Grosse Fontaine (green circles) or Undine (pink circles) parents, individuals that fall outside the cluster are marked as "no calls" (NC, grey), and the doubled haploid genotype is indicated by the black arrow. Panel G reports the relative fraction of genotyped segregating SNPs within each clustering type among the Grosse Fontaine and Undine parents, the population of their F1 progeny, as well as the two doubled haploids and their respective parents. Single cluster markers (fixed differences between paralogs) behave similarly in diploids and doubled haploids. In contrast, while diploid accessions show extensive heterozygosity at segregating loci (two- and three-cluster markers), doubled haploids show no heterozygosity.

Article Snippet: Out of 1,536 putative markers on the Miscanthus GoldenGate array (Additional file : Table S3), 1,243 showed one or more clusters in GoldenGate signal space (Figure ), indicating consistent genotyping across individuals.

Techniques:

Journal: BMC Genomics

Article Title: A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy

doi: 10.1186/1471-2164-13-142

Figure Lengend Snippet: Tetraploidy of Miscanthus relative to sorghum, with extensive colinearity and a single chromosome fusion . Panel A . Horizontal axis shows genetic map position of markers on the 19 Miscanthus linkage groups, in centiMorgans; vertical axis shows physical map position of markers aligned to the 10 sorghum chromosomes in megabases. Each dot corresponds to a single marker. Markers that could not be uniquely mapped to sorghum are shown along the horizontal axis as black dots. Duplication and colinearity of nearly all chromosomes is evident (markers in magenta). A copy of sorghum chromosome 7 (markers in sky blue) has been inserted into a copy of sorghum chromosome 4 (markers in green) to produce Miscanthus linkage group 7. Markers on Miscanthus linkage group 13, which are also syntenic with sorghum chromosome 7, are shown in a darker blue. Panel B . Circos plot showing centromeric insertion of sorghum chromosome 7 into sorghum chromosome 4 to form Miscanthus linkage group 7 (approximate boundaries indicated by arrows). Each line represents an orthologous relationship between a mapped Miscanthus marker and its unique counterpart on the Sorghum bicolor genome. Both Miscanthus linkage groups 7 and 8 have a region corresponding to sorghum chromosome 4, which is inverted with respect to the other markers (dark green arrow and lines). As also shown, Miscanthus linkage group 8 is an intact copy of sorghum chromosome 4, and Miscanthus linkage group 13 is an intact copy of sorghum chromosome 7.

Article Snippet: Out of 1,536 putative markers on the Miscanthus GoldenGate array (Additional file : Table S3), 1,243 showed one or more clusters in GoldenGate signal space (Figure ), indicating consistent genotyping across individuals.

Techniques: Marker