[Poster] Not All Exomes Are Equal: a comparison of three kits

<p>Whole exome sequencing as a protocol is highly dependent on the probe design of the kit manufacturers. Here we present results from four human patient samples run against Illumina’s Nextera, Agilent’s SureSelect v5 and Nimblegen’s SeqCap v3 library preparation kits sequenced across four lanes of a HiSeq2000. The data were processed through a variant calling pipeline based around the Genome Analysis ToolKit (GATK). A comparison is made with Illumina OmniExpressExome genotyping array data for validation. The significant differences found have a particular relevance to dermatology related studies which are an important focus for DGEM in Dundee, but also are more generally applicable to exome sequencing.</p

Additional file 2: Figure S3. of Improved annotation with de novo transcriptome assembly in four social amoeba species

Annotated domain diagrams for 16 D. discoideum developmentally relevant proteins which have had their protein sequence altered. (PDF 367 kb

Additional file 4: Table S2. of Improved annotation with de novo transcriptome assembly in four social amoeba species

List of PASAua novel genes in D. discoideum. (XLSX 13 kb

Additional file 3: Table S1. of Improved annotation with de novo transcriptome assembly in four social amoeba species

D. discoideum GFF file of genomic positions with introns < 5 bp. (TXT 9 kb

Additional file 1: Figure S1. of Improved annotation with de novo transcriptome assembly in four social amoeba species

TAGC plot for D. fasciculatum (A) and D. lacteum (B) before and after filtering. Each colour blob represents different taxa with unmatched transcripts are shaded in grey. The unannotated grey coloured transcripts after filtration set further filtered by high GC and low read coverage. This plot shows a major blob of transcripts that are annotated with the Dictyostelium fasciculatum species with high coverage and lower GC content. Other contaminations form E.coli, pseudomonas fluorescence and other species has also been highlighted with different colours. These contaminations clearly make different blobs with lower read coverage and high GC content. However, it’s good to see that there are some other transcripts that showing matched to dictyostelium discoideum- that clearly reflect the presence of some novel unannotated transcripts in the new assembly. Figure S2 A comparison of assembled transcripts read count. The boxplots represent the range between the 1st and 3rd quartiles of the data by the coloured boxes, the median is the horizontal bar and points shown beyond the whiskers are >95% of the data. Table S3 Transrate good contigs. Table S4 Olignucleotide sequences. Table S5 Alignment with DNA sequence of PCR product. (DOCX 787 kb

Single molecule RNA sequencing on small tissue volumes yields tissue-specific insights into mechanistic pathways in atopic dermatitis

<p>Figures, data and source code for paper submission.</p